HEADER ISOMERASE 22-OCT-09 3KD8 TITLE COFACTOR-INDEPENDENT PHOSPHOGLYCERATE MUTASE FROM TITLE 2 THERMOPLASMA ACIDOPHILUM DSM 1728 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT COMPND 3 PHOSPHOGLYCERATE MUTASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: PHOSPHOGLYCEROMUTASE, BPG-INDEPENDENT PGAM, APGAM; COMPND 6 EC: 5.4.2.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM; SOURCE 3 ORGANISM_TAXID: 2303; SOURCE 4 STRAIN: DSM 1728; SOURCE 5 GENE: APGM, TA0413; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS PHOSPHOGLYCERATE MUTASE, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 GENOMICS, MCSG, GLYCOLYSIS ISOMERASE, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, KEYWDS 4 GLYCOLYSIS, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.JOACHIMIAK,N.E.C.DUKE,N.MARSHALL,K.BUCK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 1 01-DEC-09 3KD8 0 JRNL AUTH A.JOACHIMIAK,N.E.C.DUKE,N.MARSHALL,K.BUCK JRNL TITL COFACTOR-INDEPENDENT PHOSPHOGLYCERATE MUTASE FROM JRNL TITL 2 THERMOPLASMA ACIDOPHILUM DSM 1728 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1305 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1758 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : -2.30000 REMARK 3 B33 (A**2) : 2.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.371 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.276 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.677 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5731 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7743 ; 1.643 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 723 ; 7.276 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 258 ;36.939 ;23.256 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 982 ;20.488 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 57 ;20.357 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 853 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4369 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3633 ; 0.786 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5836 ; 1.524 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2098 ; 2.447 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1907 ; 4.004 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. AUTHORS STATE THAT RESIDUE B58 AND B270 DO REMARK 3 NOT HAVE WELL-DEFINED SIDE CHAIN BECAUSE OF WEAK ELECTRON REMARK 3 DENSITY AT THE REGION. REMARK 4 REMARK 4 3KD8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97880, 0.97904 REMARK 200 MONOCHROMATOR : SILICON (111) REMARK 200 OPTICS : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25760 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 73.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.923 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16M MAGNESIUM CHLORIDE 0.08M REMARK 280 TRIS HCL, PH 8.5 24% PEG 4000 20% GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 43.95550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.54050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.95550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.54050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 GLY A 52 REMARK 465 ILE A 53 REMARK 465 ARG A 54 REMARK 465 CYS A 55 REMARK 465 GLY A 56 REMARK 465 SER A 57 REMARK 465 ALA A 266 REMARK 465 THR A 267 REMARK 465 GLY A 268 REMARK 465 THR A 269 REMARK 465 VAL A 270 REMARK 465 GLY A 271 REMARK 465 ASP A 299 REMARK 465 VAL A 300 REMARK 465 ALA A 301 REMARK 465 GLY A 302 REMARK 465 HIS A 303 REMARK 465 ASP A 304 REMARK 465 HIS A 339 REMARK 465 SER A 340 REMARK 465 THR A 341 REMARK 465 PRO A 342 REMARK 465 CYS A 343 REMARK 465 SER A 344 REMARK 465 PHE A 345 REMARK 465 LYS A 346 REMARK 465 ASP A 347 REMARK 465 HIS A 348 REMARK 465 SER A 349 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 SER B 50 REMARK 465 PRO B 51 REMARK 465 GLY B 52 REMARK 465 ILE B 53 REMARK 465 ARG B 54 REMARK 465 CYS B 55 REMARK 465 GLY B 56 REMARK 465 SER B 57 REMARK 465 THR B 267 REMARK 465 GLY B 268 REMARK 465 THR B 269 REMARK 465 ALA B 297 REMARK 465 THR B 298 REMARK 465 ASP B 299 REMARK 465 VAL B 300 REMARK 465 ALA B 301 REMARK 465 GLY B 302 REMARK 465 HIS B 303 REMARK 465 ASP B 304 REMARK 465 GLY B 305 REMARK 465 HIS B 339 REMARK 465 SER B 340 REMARK 465 THR B 341 REMARK 465 PRO B 342 REMARK 465 CYS B 343 REMARK 465 SER B 344 REMARK 465 PHE B 345 REMARK 465 LYS B 346 REMARK 465 ASP B 347 REMARK 465 HIS B 348 REMARK 465 SER B 349 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP B 58 CG OD1 OD2 REMARK 470 VAL B 270 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL B 356 CB VAL B 356 CG1 -0.126 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 12 -99.87 23.00 REMARK 500 ARG A 15 128.19 90.75 REMARK 500 GLN A 21 44.12 70.33 REMARK 500 ILE A 49 119.08 58.57 REMARK 500 SER A 60 -69.37 167.46 REMARK 500 ASP A 104 51.63 -145.15 REMARK 500 GLU A 142 -123.11 58.22 REMARK 500 HIS A 164 -0.72 78.54 REMARK 500 SER A 231 172.78 -56.90 REMARK 500 ASN A 273 48.03 38.34 REMARK 500 ALA A 297 32.09 -94.12 REMARK 500 ASN A 306 -169.10 -80.00 REMARK 500 ASP A 351 -51.22 141.83 REMARK 500 GLN A 393 -72.03 -60.26 REMARK 500 ALA A 395 -37.91 101.74 REMARK 500 ASP B 14 176.09 -54.80 REMARK 500 GLN B 21 42.81 73.77 REMARK 500 THR B 59 109.18 51.07 REMARK 500 ALA B 81 -58.30 113.34 REMARK 500 ARG B 103 -75.19 -84.81 REMARK 500 ASP B 104 73.65 -116.38 REMARK 500 ALA B 112 52.03 26.63 REMARK 500 GLU B 121 -56.83 128.25 REMARK 500 GLU B 142 -122.72 61.01 REMARK 500 HIS B 164 -9.31 68.14 REMARK 500 ASP B 177 154.22 164.98 REMARK 500 LYS B 250 -50.61 88.38 REMARK 500 SER B 272 -34.90 -142.55 REMARK 500 ASN B 273 58.88 -91.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 12 24.0 L L OUTSIDE RANGE REMARK 500 ASP A 14 23.7 L L OUTSIDE RANGE REMARK 500 THR B 59 25.0 L L OUTSIDE RANGE REMARK 500 HIS B 164 24.8 L L OUTSIDE RANGE REMARK 500 SER B 272 25.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IDD RELATED DB: PDB REMARK 900 3IDD IS POORER RESOLUTION THAN PRESENT EXAMPLE, ALSO A FEW REMARK 900 RESIDUES LONGER (AT BOTH N-TERM AND C-TERM ENDS) THAN THIS REMARK 900 DEPOSITION REMARK 900 RELATED ID: APC64091.1 RELATED DB: TARGETDB DBREF 3KD8 A 1 396 UNP Q9HL27 APGM_THEAC 2 397 DBREF 3KD8 B 1 396 UNP Q9HL27 APGM_THEAC 2 397 SEQADV 3KD8 SER A -2 UNP Q9HL27 EXPRESSION TAG SEQADV 3KD8 ASN A -1 UNP Q9HL27 EXPRESSION TAG SEQADV 3KD8 ALA A 0 UNP Q9HL27 EXPRESSION TAG SEQADV 3KD8 SER B -2 UNP Q9HL27 EXPRESSION TAG SEQADV 3KD8 ASN B -1 UNP Q9HL27 EXPRESSION TAG SEQADV 3KD8 ALA B 0 UNP Q9HL27 EXPRESSION TAG SEQRES 1 A 399 SER ASN ALA MSE LYS SER ILE ILE LEU ILE VAL LEU ASP SEQRES 2 A 399 GLY LEU GLY ASP ARG PRO GLY SER ASP LEU GLN ASN ARG SEQRES 3 A 399 THR PRO LEU GLN ALA ALA PHE ARG PRO ASN LEU ASN TRP SEQRES 4 A 399 LEU ALA SER HIS GLY ILE ASN GLY ILE MSE HIS PRO ILE SEQRES 5 A 399 SER PRO GLY ILE ARG CYS GLY SER ASP THR SER HIS MSE SEQRES 6 A 399 SER LEU LEU GLY TYR ASP PRO LYS VAL TYR TYR PRO GLY SEQRES 7 A 399 ARG GLY PRO PHE GLU ALA LEU GLY LEU GLY MSE ASP ILE SEQRES 8 A 399 ARG PRO GLY ASP LEU ALA PHE ARG ALA ASN PHE ALA THR SEQRES 9 A 399 ASN ARG ASP GLY VAL ILE VAL ASP ARG ARG ALA GLY ARG SEQRES 10 A 399 GLU ASN LYS GLY ASN GLU GLU LEU ALA ASP ALA ILE SER SEQRES 11 A 399 LEU ASP MSE GLY GLU TYR SER PHE ARG VAL LYS SER GLY SEQRES 12 A 399 VAL GLU HIS ARG ALA ALA LEU VAL VAL SER GLY PRO ASP SEQRES 13 A 399 LEU SER ASP MSE ILE GLY ASP SER ASP PRO HIS ARG GLU SEQRES 14 A 399 GLY LEU PRO PRO GLU LYS ILE ARG PRO THR ASP PRO SER SEQRES 15 A 399 GLY ASP ARG THR ALA GLU VAL MSE ASN ALA TYR LEU GLU SEQRES 16 A 399 GLU ALA ARG ARG ILE LEU SER ASP HIS ARG VAL ASN LYS SEQRES 17 A 399 GLU ARG VAL LYS ASN GLY ARG LEU PRO GLY ASN GLU LEU SEQRES 18 A 399 LEU VAL ARG SER ALA GLY LYS VAL PRO ALA ILE PRO SER SEQRES 19 A 399 PHE THR GLU LYS ASN ARG MSE LYS GLY ALA CYS VAL VAL SEQRES 20 A 399 GLY SER PRO TRP LEU LYS GLY LEU CYS ARG LEU LEU ARG SEQRES 21 A 399 MSE ASP VAL PHE ASP VAL PRO GLY ALA THR GLY THR VAL SEQRES 22 A 399 GLY SER ASN TYR ARG GLY LYS ILE GLU LYS ALA VAL ASP SEQRES 23 A 399 LEU THR SER SER HIS ASP PHE VAL LEU VAL ASN ILE LYS SEQRES 24 A 399 ALA THR ASP VAL ALA GLY HIS ASP GLY ASN TYR PRO LEU SEQRES 25 A 399 LYS ARG ASP VAL ILE GLU ASP ILE ASP ARG ALA MSE GLU SEQRES 26 A 399 PRO LEU LYS SER ILE GLY ASP HIS ALA VAL ILE CYS VAL SEQRES 27 A 399 THR GLY ASP HIS SER THR PRO CYS SER PHE LYS ASP HIS SEQRES 28 A 399 SER GLY ASP PRO VAL PRO ILE VAL PHE TYR THR ASP GLY SEQRES 29 A 399 VAL MSE ASN ASP GLY VAL HIS LEU PHE ASP GLU LEU SER SEQRES 30 A 399 SER ALA SER GLY SER LEU ARG ILE THR SER TYR ASN VAL SEQRES 31 A 399 MSE ASP ILE LEU MSE GLN LEU ALA GLY SEQRES 1 B 399 SER ASN ALA MSE LYS SER ILE ILE LEU ILE VAL LEU ASP SEQRES 2 B 399 GLY LEU GLY ASP ARG PRO GLY SER ASP LEU GLN ASN ARG SEQRES 3 B 399 THR PRO LEU GLN ALA ALA PHE ARG PRO ASN LEU ASN TRP SEQRES 4 B 399 LEU ALA SER HIS GLY ILE ASN GLY ILE MSE HIS PRO ILE SEQRES 5 B 399 SER PRO GLY ILE ARG CYS GLY SER ASP THR SER HIS MSE SEQRES 6 B 399 SER LEU LEU GLY TYR ASP PRO LYS VAL TYR TYR PRO GLY SEQRES 7 B 399 ARG GLY PRO PHE GLU ALA LEU GLY LEU GLY MSE ASP ILE SEQRES 8 B 399 ARG PRO GLY ASP LEU ALA PHE ARG ALA ASN PHE ALA THR SEQRES 9 B 399 ASN ARG ASP GLY VAL ILE VAL ASP ARG ARG ALA GLY ARG SEQRES 10 B 399 GLU ASN LYS GLY ASN GLU GLU LEU ALA ASP ALA ILE SER SEQRES 11 B 399 LEU ASP MSE GLY GLU TYR SER PHE ARG VAL LYS SER GLY SEQRES 12 B 399 VAL GLU HIS ARG ALA ALA LEU VAL VAL SER GLY PRO ASP SEQRES 13 B 399 LEU SER ASP MSE ILE GLY ASP SER ASP PRO HIS ARG GLU SEQRES 14 B 399 GLY LEU PRO PRO GLU LYS ILE ARG PRO THR ASP PRO SER SEQRES 15 B 399 GLY ASP ARG THR ALA GLU VAL MSE ASN ALA TYR LEU GLU SEQRES 16 B 399 GLU ALA ARG ARG ILE LEU SER ASP HIS ARG VAL ASN LYS SEQRES 17 B 399 GLU ARG VAL LYS ASN GLY ARG LEU PRO GLY ASN GLU LEU SEQRES 18 B 399 LEU VAL ARG SER ALA GLY LYS VAL PRO ALA ILE PRO SER SEQRES 19 B 399 PHE THR GLU LYS ASN ARG MSE LYS GLY ALA CYS VAL VAL SEQRES 20 B 399 GLY SER PRO TRP LEU LYS GLY LEU CYS ARG LEU LEU ARG SEQRES 21 B 399 MSE ASP VAL PHE ASP VAL PRO GLY ALA THR GLY THR VAL SEQRES 22 B 399 GLY SER ASN TYR ARG GLY LYS ILE GLU LYS ALA VAL ASP SEQRES 23 B 399 LEU THR SER SER HIS ASP PHE VAL LEU VAL ASN ILE LYS SEQRES 24 B 399 ALA THR ASP VAL ALA GLY HIS ASP GLY ASN TYR PRO LEU SEQRES 25 B 399 LYS ARG ASP VAL ILE GLU ASP ILE ASP ARG ALA MSE GLU SEQRES 26 B 399 PRO LEU LYS SER ILE GLY ASP HIS ALA VAL ILE CYS VAL SEQRES 27 B 399 THR GLY ASP HIS SER THR PRO CYS SER PHE LYS ASP HIS SEQRES 28 B 399 SER GLY ASP PRO VAL PRO ILE VAL PHE TYR THR ASP GLY SEQRES 29 B 399 VAL MSE ASN ASP GLY VAL HIS LEU PHE ASP GLU LEU SER SEQRES 30 B 399 SER ALA SER GLY SER LEU ARG ILE THR SER TYR ASN VAL SEQRES 31 B 399 MSE ASP ILE LEU MSE GLN LEU ALA GLY MODRES 3KD8 MSE A 1 MET SELENOMETHIONINE MODRES 3KD8 MSE A 46 MET SELENOMETHIONINE MODRES 3KD8 MSE A 62 MET SELENOMETHIONINE MODRES 3KD8 MSE A 86 MET SELENOMETHIONINE MODRES 3KD8 MSE A 130 MET SELENOMETHIONINE MODRES 3KD8 MSE A 157 MET SELENOMETHIONINE MODRES 3KD8 MSE A 187 MET SELENOMETHIONINE MODRES 3KD8 MSE A 238 MET SELENOMETHIONINE MODRES 3KD8 MSE A 258 MET SELENOMETHIONINE MODRES 3KD8 MSE A 321 MET SELENOMETHIONINE MODRES 3KD8 MSE A 363 MET SELENOMETHIONINE MODRES 3KD8 MSE A 388 MET SELENOMETHIONINE MODRES 3KD8 MSE A 392 MET SELENOMETHIONINE MODRES 3KD8 MSE B 1 MET SELENOMETHIONINE MODRES 3KD8 MSE B 46 MET SELENOMETHIONINE MODRES 3KD8 MSE B 62 MET SELENOMETHIONINE MODRES 3KD8 MSE B 86 MET SELENOMETHIONINE MODRES 3KD8 MSE B 130 MET SELENOMETHIONINE MODRES 3KD8 MSE B 157 MET SELENOMETHIONINE MODRES 3KD8 MSE B 187 MET SELENOMETHIONINE MODRES 3KD8 MSE B 238 MET SELENOMETHIONINE MODRES 3KD8 MSE B 258 MET SELENOMETHIONINE MODRES 3KD8 MSE B 321 MET SELENOMETHIONINE MODRES 3KD8 MSE B 363 MET SELENOMETHIONINE MODRES 3KD8 MSE B 388 MET SELENOMETHIONINE MODRES 3KD8 MSE B 392 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 46 8 HET MSE A 62 8 HET MSE A 86 8 HET MSE A 130 8 HET MSE A 157 8 HET MSE A 187 8 HET MSE A 238 8 HET MSE A 258 8 HET MSE A 321 8 HET MSE A 363 8 HET MSE A 388 8 HET MSE A 392 8 HET MSE B 1 8 HET MSE B 46 8 HET MSE B 62 8 HET MSE B 86 8 HET MSE B 130 8 HET MSE B 157 8 HET MSE B 187 8 HET MSE B 238 8 HET MSE B 258 8 HET MSE B 321 8 HET MSE B 363 8 HET MSE B 388 8 HET MSE B 392 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 26(C5 H11 N O2 SE) FORMUL 3 HOH *145(H2 O) HELIX 1 1 THR A 24 ALA A 29 1 6 HELIX 2 2 ARG A 31 HIS A 40 1 10 HELIX 3 3 SER A 60 LEU A 65 1 6 HELIX 4 4 ASP A 68 TYR A 73 1 6 HELIX 5 5 GLY A 75 LEU A 84 1 10 HELIX 6 6 ARG A 111 GLU A 115 5 5 HELIX 7 7 GLY A 118 ILE A 126 1 9 HELIX 8 8 ASP A 177 SER A 179 5 3 HELIX 9 9 GLY A 180 ASP A 200 1 21 HELIX 10 10 HIS A 201 ASN A 210 1 10 HELIX 11 11 SER A 231 ARG A 237 1 7 HELIX 12 12 SER A 246 LEU A 256 1 11 HELIX 13 13 ASN A 273 THR A 285 1 13 HELIX 14 14 ASN A 306 ALA A 320 1 15 HELIX 15 15 MSE A 321 SER A 326 5 6 HELIX 16 16 SER A 374 GLY A 378 5 5 HELIX 17 17 ASN A 386 LEU A 394 1 9 HELIX 18 18 GLY B 17 GLN B 21 5 5 HELIX 19 19 THR B 24 ALA B 29 1 6 HELIX 20 20 ARG B 31 HIS B 40 1 10 HELIX 21 21 SER B 60 LEU B 65 1 6 HELIX 22 22 ASP B 68 TYR B 73 1 6 HELIX 23 23 GLY B 75 GLY B 83 1 9 HELIX 24 24 ARG B 111 GLU B 115 5 5 HELIX 25 25 GLY B 118 ILE B 126 1 9 HELIX 26 26 ASP B 177 SER B 179 5 3 HELIX 27 27 GLY B 180 ASP B 200 1 21 HELIX 28 28 HIS B 201 ASN B 210 1 10 HELIX 29 29 SER B 231 ARG B 237 1 7 HELIX 30 30 PRO B 247 LEU B 256 1 10 HELIX 31 31 ASN B 273 HIS B 288 1 16 HELIX 32 32 ASN B 306 MSE B 321 1 16 HELIX 33 33 GLU B 322 ILE B 327 5 6 HELIX 34 34 LEU B 373 GLY B 378 5 6 HELIX 35 35 ASN B 386 GLY B 396 1 11 SHEET 1 A 8 ASP A 259 PHE A 261 0 SHEET 2 A 8 GLY A 240 VAL A 243 1 N CYS A 242 O PHE A 261 SHEET 3 A 8 PHE A 290 LYS A 296 1 O LEU A 292 N VAL A 243 SHEET 4 A 8 SER A 3 ASP A 10 1 N ASP A 10 O ILE A 295 SHEET 5 A 8 ALA A 331 ASP A 338 1 O THR A 336 N LEU A 9 SHEET 6 A 8 VAL A 353 THR A 359 -1 O TYR A 358 N ILE A 333 SHEET 7 A 8 ILE A 42 HIS A 47 -1 N MSE A 46 O VAL A 353 SHEET 8 A 8 LEU A 380 THR A 383 1 O ILE A 382 N HIS A 47 SHEET 1 B 5 ILE A 107 ASP A 109 0 SHEET 2 B 5 LEU A 93 ASN A 102 -1 N THR A 101 O ASP A 109 SHEET 3 B 5 ARG A 144 SER A 150 -1 O VAL A 149 N LEU A 93 SHEET 4 B 5 TYR A 133 SER A 139 -1 N ARG A 136 O VAL A 148 SHEET 5 B 5 LEU A 128 MSE A 130 -1 N LEU A 128 O PHE A 135 SHEET 1 C 3 ILE A 107 ASP A 109 0 SHEET 2 C 3 LEU A 93 ASN A 102 -1 N THR A 101 O ASP A 109 SHEET 3 C 3 GLU A 217 LYS A 225 -1 O GLU A 217 N ALA A 100 SHEET 1 D 8 ASP B 259 VAL B 260 0 SHEET 2 D 8 GLY B 240 VAL B 243 1 N CYS B 242 O ASP B 259 SHEET 3 D 8 PHE B 290 ILE B 295 1 O LEU B 292 N VAL B 243 SHEET 4 D 8 SER B 3 LEU B 9 1 N ILE B 4 O VAL B 291 SHEET 5 D 8 ALA B 331 GLY B 337 1 O CYS B 334 N ILE B 7 SHEET 6 D 8 VAL B 353 TYR B 358 -1 O TYR B 358 N ILE B 333 SHEET 7 D 8 ILE B 42 HIS B 47 -1 N MSE B 46 O VAL B 353 SHEET 8 D 8 LEU B 380 THR B 383 1 O LEU B 380 N ASN B 43 SHEET 1 E 5 ILE B 107 ASP B 109 0 SHEET 2 E 5 LEU B 93 ASN B 102 -1 N THR B 101 O ASP B 109 SHEET 3 E 5 ARG B 144 SER B 150 -1 O VAL B 149 N LEU B 93 SHEET 4 E 5 TYR B 133 SER B 139 -1 N SER B 134 O SER B 150 SHEET 5 E 5 LEU B 128 MSE B 130 -1 N MSE B 130 O TYR B 133 SHEET 1 F 3 ILE B 107 ASP B 109 0 SHEET 2 F 3 LEU B 93 ASN B 102 -1 N THR B 101 O ASP B 109 SHEET 3 F 3 GLU B 217 LYS B 225 -1 O LEU B 219 N ASN B 98 SSBOND 1 CYS A 242 CYS A 253 1555 1555 2.06 SSBOND 2 CYS B 242 CYS B 253 1555 1555 2.04 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C ILE A 45 N MSE A 46 1555 1555 1.32 LINK C MSE A 46 N HIS A 47 1555 1555 1.33 LINK C HIS A 61 N MSE A 62 1555 1555 1.32 LINK C MSE A 62 N SER A 63 1555 1555 1.33 LINK C GLY A 85 N MSE A 86 1555 1555 1.34 LINK C MSE A 86 N ASP A 87 1555 1555 1.33 LINK C ASP A 129 N MSE A 130 1555 1555 1.32 LINK C MSE A 130 N GLY A 131 1555 1555 1.33 LINK C ASP A 156 N MSE A 157 1555 1555 1.33 LINK C MSE A 157 N ILE A 158 1555 1555 1.33 LINK C VAL A 186 N MSE A 187 1555 1555 1.34 LINK C MSE A 187 N ASN A 188 1555 1555 1.33 LINK C ARG A 237 N MSE A 238 1555 1555 1.33 LINK C MSE A 238 N LYS A 239 1555 1555 1.32 LINK C ARG A 257 N MSE A 258 1555 1555 1.33 LINK C MSE A 258 N ASP A 259 1555 1555 1.33 LINK C ALA A 320 N MSE A 321 1555 1555 1.32 LINK C MSE A 321 N GLU A 322 1555 1555 1.33 LINK C VAL A 362 N MSE A 363 1555 1555 1.32 LINK C MSE A 363 N ASN A 364 1555 1555 1.33 LINK C VAL A 387 N MSE A 388 1555 1555 1.33 LINK C MSE A 388 N ASP A 389 1555 1555 1.33 LINK C LEU A 391 N MSE A 392 1555 1555 1.34 LINK C MSE A 392 N GLN A 393 1555 1555 1.33 LINK C MSE B 1 N LYS B 2 1555 1555 1.33 LINK C ILE B 45 N MSE B 46 1555 1555 1.33 LINK C MSE B 46 N HIS B 47 1555 1555 1.33 LINK C HIS B 61 N MSE B 62 1555 1555 1.32 LINK C MSE B 62 N SER B 63 1555 1555 1.32 LINK C GLY B 85 N MSE B 86 1555 1555 1.34 LINK C MSE B 86 N ASP B 87 1555 1555 1.33 LINK C ASP B 129 N MSE B 130 1555 1555 1.33 LINK C MSE B 130 N GLY B 131 1555 1555 1.34 LINK C ASP B 156 N MSE B 157 1555 1555 1.34 LINK C MSE B 157 N ILE B 158 1555 1555 1.33 LINK C VAL B 186 N MSE B 187 1555 1555 1.33 LINK C MSE B 187 N ASN B 188 1555 1555 1.34 LINK C ARG B 237 N MSE B 238 1555 1555 1.33 LINK C MSE B 238 N LYS B 239 1555 1555 1.33 LINK C ARG B 257 N MSE B 258 1555 1555 1.33 LINK C MSE B 258 N ASP B 259 1555 1555 1.33 LINK C ALA B 320 N MSE B 321 1555 1555 1.33 LINK C MSE B 321 N GLU B 322 1555 1555 1.32 LINK C VAL B 362 N MSE B 363 1555 1555 1.33 LINK C MSE B 363 N ASN B 364 1555 1555 1.33 LINK C VAL B 387 N MSE B 388 1555 1555 1.33 LINK C MSE B 388 N ASP B 389 1555 1555 1.33 LINK C LEU B 391 N MSE B 392 1555 1555 1.33 LINK C MSE B 392 N GLN B 393 1555 1555 1.32 CRYST1 87.911 137.081 67.088 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011375 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014906 0.00000 HETATM 1 N MSE A 1 38.310 44.501 96.256 1.00 48.03 N HETATM 2 CA MSE A 1 39.141 43.855 97.312 1.00 48.51 C HETATM 3 C MSE A 1 39.810 42.533 96.872 1.00 46.64 C HETATM 4 O MSE A 1 39.455 41.947 95.841 1.00 46.92 O HETATM 5 CB MSE A 1 38.285 43.605 98.555 1.00 49.70 C HETATM 6 CG MSE A 1 37.194 42.554 98.345 1.00 55.21 C HETATM 7 SE MSE A 1 36.037 42.345 99.913 1.00 68.70 SE HETATM 8 CE MSE A 1 35.099 40.724 99.308 1.00 64.00 C