HEADER TRANSFERASE 19-MAR-09 3GOS TITLE THE CRYSTAL STRUCTURE OF 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N- TITLE 2 SUCCINYLTRANSFERASE FROM YERSINIA PESTIS CO92 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- COMPND 3 SUCCINYLTRANSFERASE; COMPND 4 CHAIN: A, B, C; COMPND 5 SYNONYM: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE, THP COMPND 6 SUCCINYLTRANSFERASE, TETRAHYDROPICOLINATE SUCCINYLASE; COMPND 7 EC: 2.3.1.117; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 STRAIN: CO92; SOURCE 5 GENE: DAPD, GI: 16121341, Y3140, YPO1041, YP_2810; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19C KEYWDS 2, 3, 4, 5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE, KEYWDS 2 ACYLTRANSFERASE, AMINO-ACID BIOSYNTHESIS, DIAMINOPIMELATE KEYWDS 3 BIOSYNTHESIS, LYSINE BIOSYNTHESIS, TRANSFERASE, STRUCTURAL GENOMICS, KEYWDS 4 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,N.MALTSEVA,K.KWON,W.ANDERSON,A.JOACHIMIAK,CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 3 06-SEP-23 3GOS 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3GOS 1 VERSN REVDAT 1 12-MAY-09 3GOS 0 JRNL AUTH R.ZHANG,N.MALTSEVA,K.KWON,W.ANDERSON,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF JRNL TITL 2 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE JRNL TITL 3 N-SUCCINYLTRANSFERASE FROM YERSINIA PESTIS CO92 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0054 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 70583 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3741 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4750 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6288 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 285 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23000 REMARK 3 B22 (A**2) : -1.84000 REMARK 3 B33 (A**2) : 1.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.77000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.206 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6441 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4286 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8740 ; 1.830 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10439 ; 1.018 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 825 ; 7.397 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;35.684 ;23.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1078 ;16.045 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;16.520 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1014 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7252 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1302 ; 0.001 ; 0.020 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): 4086 ; 1.097 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1704 ; 0.362 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6613 ; 1.751 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2355 ; 2.881 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2127 ; 4.243 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 18 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -1 A 50 REMARK 3 RESIDUE RANGE : A 51 A 100 REMARK 3 RESIDUE RANGE : A 101 A 150 REMARK 3 RESIDUE RANGE : A 151 A 200 REMARK 3 RESIDUE RANGE : A 201 A 256 REMARK 3 RESIDUE RANGE : A 257 A 274 REMARK 3 RESIDUE RANGE : B -1 B 50 REMARK 3 RESIDUE RANGE : B 51 B 100 REMARK 3 RESIDUE RANGE : B 101 B 150 REMARK 3 RESIDUE RANGE : B 151 B 200 REMARK 3 RESIDUE RANGE : B 201 B 256 REMARK 3 RESIDUE RANGE : B 257 B 274 REMARK 3 RESIDUE RANGE : C -1 C 50 REMARK 3 RESIDUE RANGE : C 51 C 100 REMARK 3 RESIDUE RANGE : C 101 C 150 REMARK 3 RESIDUE RANGE : C 151 C 200 REMARK 3 RESIDUE RANGE : C 201 C 256 REMARK 3 RESIDUE RANGE : C 257 C 274 REMARK 3 ORIGIN FOR THE GROUP (A): -31.4660 7.6960 26.2180 REMARK 3 T TENSOR REMARK 3 T11: 0.0473 T22: 0.0826 REMARK 3 T33: 0.0328 T12: -0.0013 REMARK 3 T13: -0.0287 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.2314 L22: 0.2818 REMARK 3 L33: 0.1226 L12: -0.0186 REMARK 3 L13: -0.0879 L23: 0.0164 REMARK 3 S TENSOR REMARK 3 S11: -0.0027 S12: -0.0119 S13: 0.0138 REMARK 3 S21: 0.0313 S22: -0.0059 S23: 0.0222 REMARK 3 S31: 0.0175 S32: 0.0184 S33: 0.0086 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3GOS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 57.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: PDB ENTRY 3TDT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG3000, 0.1M CACODINATE, 0.2M REMARK 280 MGCL2, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.84750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 LYS A 259 REMARK 465 THR A 260 REMARK 465 ARG A 261 REMARK 465 SER A 262 REMARK 465 LYS A 263 REMARK 465 VAL A 264 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 GLU A 13 CG CD OE1 OE2 REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 GLU B 13 CG CD OE1 OE2 REMARK 470 LYS B 241 CG CD CE NZ REMARK 470 LYS C 241 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N GLN C -1 O HOH C 285 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP B 24 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 104 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG B 104 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP B 216 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG C 15 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 ALA A 78 -94.53 64.69 REMARK 500 PRO A 108 42.05 -100.78 REMARK 500 ASP A 257 -71.77 -53.73 REMARK 500 ARG A 271 -5.32 -52.15 REMARK 500 ALA B 78 -89.70 75.21 REMARK 500 TYR B 93 135.26 -37.66 REMARK 500 CYS B 149 -2.96 77.32 REMARK 500 SER B 203 -159.05 -84.69 REMARK 500 ALA C 78 -84.27 74.94 REMARK 500 PRO C 108 38.30 -95.08 REMARK 500 SER C 126 174.30 178.47 REMARK 500 CYS C 149 -2.60 72.11 REMARK 500 LEU C 168 -82.57 -110.75 REMARK 500 PRO C 175 -178.43 -68.47 REMARK 500 LYS C 259 175.49 171.16 REMARK 500 ILE C 273 151.29 -47.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 275 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 346 O REMARK 620 2 HOH A 380 O 73.8 REMARK 620 3 HOH B 293 O 96.2 98.1 REMARK 620 4 HOH C 284 O 175.6 101.9 83.4 REMARK 620 5 HOH C 317 O 93.8 164.6 92.3 90.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 275 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP00571 RELATED DB: TARGETDB DBREF 3GOS A 1 274 UNP Q8ZH69 DAPD_YERPE 1 274 DBREF 3GOS B 1 274 UNP Q8ZH69 DAPD_YERPE 1 274 DBREF 3GOS C 1 274 UNP Q8ZH69 DAPD_YERPE 1 274 SEQADV 3GOS GLN A -1 UNP Q8ZH69 EXPRESSION TAG SEQADV 3GOS SER A 0 UNP Q8ZH69 EXPRESSION TAG SEQADV 3GOS GLN B -1 UNP Q8ZH69 EXPRESSION TAG SEQADV 3GOS SER B 0 UNP Q8ZH69 EXPRESSION TAG SEQADV 3GOS GLN C -1 UNP Q8ZH69 EXPRESSION TAG SEQADV 3GOS SER C 0 UNP Q8ZH69 EXPRESSION TAG SEQRES 1 A 276 GLN SER MET GLN GLN LEU GLN ASN VAL ILE GLU THR ALA SEQRES 2 A 276 PHE GLU ARG ARG ALA ASP ILE THR PRO ALA ASN VAL ASP SEQRES 3 A 276 THR VAL THR ARG GLU ALA ILE THR HIS VAL ILE ASP LEU SEQRES 4 A 276 LEU ASP THR GLY ALA LEU ARG VAL ALA GLU LYS ILE ASP SEQRES 5 A 276 GLY GLN TRP VAL THR HIS GLN TRP LEU LYS LYS ALA VAL SEQRES 6 A 276 LEU LEU SER PHE ARG ILE ASN ASP ASN GLN VAL MET GLU SEQRES 7 A 276 GLY ALA GLU THR ARG TYR TYR ASP LYS VAL PRO MET LYS SEQRES 8 A 276 PHE ALA GLY TYR ASP GLU ALA ARG PHE GLN ARG GLU GLY SEQRES 9 A 276 PHE ARG VAL VAL PRO PRO ALA THR VAL ARG LYS GLY ALA SEQRES 10 A 276 PHE ILE ALA ARG ASN THR VAL LEU MET PRO SER TYR VAL SEQRES 11 A 276 ASN ILE GLY ALA PHE VAL ASP GLU GLY THR MET VAL ASP SEQRES 12 A 276 THR TRP ALA THR VAL GLY SER CYS ALA GLN ILE GLY LYS SEQRES 13 A 276 ASN VAL HIS LEU SER GLY GLY VAL GLY ILE GLY GLY VAL SEQRES 14 A 276 LEU GLU PRO LEU GLN ALA ASN PRO THR ILE ILE GLU ASP SEQRES 15 A 276 ASN CYS PHE VAL GLY ALA ARG SER GLU VAL VAL GLU GLY SEQRES 16 A 276 VAL ILE VAL GLU GLU GLY SER VAL ILE SER MET GLY VAL SEQRES 17 A 276 PHE ILE GLY GLN SER THR ARG ILE TYR ASP ARG GLU THR SEQRES 18 A 276 GLY GLU VAL HIS TYR GLY ARG VAL PRO ALA GLY SER VAL SEQRES 19 A 276 VAL VAL SER GLY ASN LEU PRO SER LYS ASP GLY SER TYR SEQRES 20 A 276 SER LEU TYR CYS ALA VAL ILE VAL LYS LYS VAL ASP ALA SEQRES 21 A 276 LYS THR ARG SER LYS VAL GLY ILE ASN GLU LEU LEU ARG SEQRES 22 A 276 THR ILE ASP SEQRES 1 B 276 GLN SER MET GLN GLN LEU GLN ASN VAL ILE GLU THR ALA SEQRES 2 B 276 PHE GLU ARG ARG ALA ASP ILE THR PRO ALA ASN VAL ASP SEQRES 3 B 276 THR VAL THR ARG GLU ALA ILE THR HIS VAL ILE ASP LEU SEQRES 4 B 276 LEU ASP THR GLY ALA LEU ARG VAL ALA GLU LYS ILE ASP SEQRES 5 B 276 GLY GLN TRP VAL THR HIS GLN TRP LEU LYS LYS ALA VAL SEQRES 6 B 276 LEU LEU SER PHE ARG ILE ASN ASP ASN GLN VAL MET GLU SEQRES 7 B 276 GLY ALA GLU THR ARG TYR TYR ASP LYS VAL PRO MET LYS SEQRES 8 B 276 PHE ALA GLY TYR ASP GLU ALA ARG PHE GLN ARG GLU GLY SEQRES 9 B 276 PHE ARG VAL VAL PRO PRO ALA THR VAL ARG LYS GLY ALA SEQRES 10 B 276 PHE ILE ALA ARG ASN THR VAL LEU MET PRO SER TYR VAL SEQRES 11 B 276 ASN ILE GLY ALA PHE VAL ASP GLU GLY THR MET VAL ASP SEQRES 12 B 276 THR TRP ALA THR VAL GLY SER CYS ALA GLN ILE GLY LYS SEQRES 13 B 276 ASN VAL HIS LEU SER GLY GLY VAL GLY ILE GLY GLY VAL SEQRES 14 B 276 LEU GLU PRO LEU GLN ALA ASN PRO THR ILE ILE GLU ASP SEQRES 15 B 276 ASN CYS PHE VAL GLY ALA ARG SER GLU VAL VAL GLU GLY SEQRES 16 B 276 VAL ILE VAL GLU GLU GLY SER VAL ILE SER MET GLY VAL SEQRES 17 B 276 PHE ILE GLY GLN SER THR ARG ILE TYR ASP ARG GLU THR SEQRES 18 B 276 GLY GLU VAL HIS TYR GLY ARG VAL PRO ALA GLY SER VAL SEQRES 19 B 276 VAL VAL SER GLY ASN LEU PRO SER LYS ASP GLY SER TYR SEQRES 20 B 276 SER LEU TYR CYS ALA VAL ILE VAL LYS LYS VAL ASP ALA SEQRES 21 B 276 LYS THR ARG SER LYS VAL GLY ILE ASN GLU LEU LEU ARG SEQRES 22 B 276 THR ILE ASP SEQRES 1 C 276 GLN SER MET GLN GLN LEU GLN ASN VAL ILE GLU THR ALA SEQRES 2 C 276 PHE GLU ARG ARG ALA ASP ILE THR PRO ALA ASN VAL ASP SEQRES 3 C 276 THR VAL THR ARG GLU ALA ILE THR HIS VAL ILE ASP LEU SEQRES 4 C 276 LEU ASP THR GLY ALA LEU ARG VAL ALA GLU LYS ILE ASP SEQRES 5 C 276 GLY GLN TRP VAL THR HIS GLN TRP LEU LYS LYS ALA VAL SEQRES 6 C 276 LEU LEU SER PHE ARG ILE ASN ASP ASN GLN VAL MET GLU SEQRES 7 C 276 GLY ALA GLU THR ARG TYR TYR ASP LYS VAL PRO MET LYS SEQRES 8 C 276 PHE ALA GLY TYR ASP GLU ALA ARG PHE GLN ARG GLU GLY SEQRES 9 C 276 PHE ARG VAL VAL PRO PRO ALA THR VAL ARG LYS GLY ALA SEQRES 10 C 276 PHE ILE ALA ARG ASN THR VAL LEU MET PRO SER TYR VAL SEQRES 11 C 276 ASN ILE GLY ALA PHE VAL ASP GLU GLY THR MET VAL ASP SEQRES 12 C 276 THR TRP ALA THR VAL GLY SER CYS ALA GLN ILE GLY LYS SEQRES 13 C 276 ASN VAL HIS LEU SER GLY GLY VAL GLY ILE GLY GLY VAL SEQRES 14 C 276 LEU GLU PRO LEU GLN ALA ASN PRO THR ILE ILE GLU ASP SEQRES 15 C 276 ASN CYS PHE VAL GLY ALA ARG SER GLU VAL VAL GLU GLY SEQRES 16 C 276 VAL ILE VAL GLU GLU GLY SER VAL ILE SER MET GLY VAL SEQRES 17 C 276 PHE ILE GLY GLN SER THR ARG ILE TYR ASP ARG GLU THR SEQRES 18 C 276 GLY GLU VAL HIS TYR GLY ARG VAL PRO ALA GLY SER VAL SEQRES 19 C 276 VAL VAL SER GLY ASN LEU PRO SER LYS ASP GLY SER TYR SEQRES 20 C 276 SER LEU TYR CYS ALA VAL ILE VAL LYS LYS VAL ASP ALA SEQRES 21 C 276 LYS THR ARG SER LYS VAL GLY ILE ASN GLU LEU LEU ARG SEQRES 22 C 276 THR ILE ASP HET MG A 275 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ FORMUL 5 HOH *285(H2 O) HELIX 1 1 GLN A -1 ARG A 14 1 16 HELIX 2 2 ARG A 15 ILE A 18 5 4 HELIX 3 3 ASP A 24 THR A 40 1 17 HELIX 4 4 HIS A 56 ILE A 69 1 14 HELIX 5 5 ASP A 94 GLY A 102 1 9 HELIX 6 6 GLY A 265 ARG A 271 1 7 HELIX 7 7 GLN B -1 ARG B 14 1 16 HELIX 8 8 ARG B 15 ILE B 18 5 4 HELIX 9 9 ASP B 24 THR B 40 1 17 HELIX 10 10 HIS B 56 ILE B 69 1 14 HELIX 11 11 MET B 88 GLY B 92 5 5 HELIX 12 12 ASP B 94 GLY B 102 1 9 HELIX 13 13 SER B 262 ARG B 271 1 10 HELIX 14 14 GLN C -1 ARG C 14 1 16 HELIX 15 15 ARG C 15 ILE C 18 5 4 HELIX 16 16 ASP C 24 THR C 40 1 17 HELIX 17 17 HIS C 56 ILE C 69 1 14 HELIX 18 18 MET C 88 GLY C 92 5 5 HELIX 19 19 ASP C 94 GLY C 102 1 9 HELIX 20 20 SER C 262 THR C 272 1 11 SHEET 1 A 2 ALA A 46 ILE A 49 0 SHEET 2 A 2 GLN A 52 THR A 55 -1 O GLN A 52 N ILE A 49 SHEET 1 B 2 GLN A 73 GLY A 77 0 SHEET 2 B 2 THR A 80 ASP A 84 -1 O TYR A 82 N MET A 75 SHEET 1 C10 ARG A 104 VAL A 105 0 SHEET 2 C10 VAL A 122 LEU A 123 1 O LEU A 123 N ARG A 104 SHEET 3 C10 MET A 139 VAL A 140 1 O VAL A 140 N VAL A 122 SHEET 4 C10 HIS A 157 LEU A 158 1 O LEU A 158 N MET A 139 SHEET 5 C10 PHE A 183 VAL A 184 1 O VAL A 184 N HIS A 157 SHEET 6 C10 VAL A 201 ILE A 202 1 O ILE A 202 N PHE A 183 SHEET 7 C10 SER A 231 PRO A 239 1 O VAL A 233 N VAL A 201 SHEET 8 C10 SER C 246 LYS C 255 -1 O SER C 246 N ASN A 237 SHEET 9 C10 ILE C 214 ASP C 216 1 N TYR C 215 O ALA C 250 SHEET 10 C10 GLU C 221 HIS C 223 -1 O HIS C 223 N ILE C 214 SHEET 1 D 7 VAL A 222 HIS A 223 0 SHEET 2 D 7 ILE A 214 ASP A 216 -1 N ILE A 214 O HIS A 223 SHEET 3 D 7 SER A 246 LYS A 255 1 O ALA A 250 N TYR A 215 SHEET 4 D 7 SER B 231 PRO B 239 -1 O SER B 235 N TYR A 248 SHEET 5 D 7 SER B 246 LYS B 255 -1 O LYS B 254 N VAL B 232 SHEET 6 D 7 ILE B 214 ASP B 216 1 N TYR B 215 O ILE B 252 SHEET 7 D 7 VAL B 222 HIS B 223 -1 O HIS B 223 N ILE B 214 SHEET 1 E12 ARG B 104 VAL B 105 0 SHEET 2 E12 VAL B 122 LEU B 123 1 O LEU B 123 N ARG B 104 SHEET 3 E12 MET B 139 VAL B 140 1 O VAL B 140 N VAL B 122 SHEET 4 E12 HIS B 157 LEU B 158 1 O LEU B 158 N MET B 139 SHEET 5 E12 PHE B 183 VAL B 184 1 O VAL B 184 N HIS B 157 SHEET 6 E12 VAL B 201 ILE B 202 1 O ILE B 202 N PHE B 183 SHEET 7 E12 SER B 231 PRO B 239 1 O VAL B 233 N VAL B 201 SHEET 8 E12 SER B 246 LYS B 255 -1 O LYS B 254 N VAL B 232 SHEET 9 E12 SER C 231 PRO C 239 -1 O SER C 235 N TYR B 248 SHEET 10 E12 SER C 246 LYS C 255 -1 O LYS C 254 N VAL C 232 SHEET 11 E12 ILE C 214 ASP C 216 1 N TYR C 215 O ALA C 250 SHEET 12 E12 GLU C 221 HIS C 223 -1 O HIS C 223 N ILE C 214 SHEET 1 F10 ARG C 104 VAL C 105 0 SHEET 2 F10 VAL C 122 LEU C 123 1 O LEU C 123 N ARG C 104 SHEET 3 F10 MET C 139 VAL C 140 1 O VAL C 140 N VAL C 122 SHEET 4 F10 HIS C 157 LEU C 158 1 O LEU C 158 N MET C 139 SHEET 5 F10 PHE C 183 VAL C 184 1 O VAL C 184 N HIS C 157 SHEET 6 F10 VAL C 201 ILE C 202 1 O ILE C 202 N PHE C 183 SHEET 7 F10 SER C 231 PRO C 239 1 O VAL C 233 N VAL C 201 SHEET 8 F10 SER B 246 LYS B 255 -1 N TYR B 248 O SER C 235 SHEET 9 F10 ILE B 214 ASP B 216 1 N TYR B 215 O ILE B 252 SHEET 10 F10 VAL B 222 HIS B 223 -1 O HIS B 223 N ILE B 214 SHEET 1 G 6 THR A 110 VAL A 111 0 SHEET 2 G 6 SER A 126 VAL A 128 1 O SER A 126 N THR A 110 SHEET 3 G 6 ALA A 144 VAL A 146 1 O VAL A 146 N TYR A 127 SHEET 4 G 6 GLY A 163 ILE A 164 1 O ILE A 164 N THR A 145 SHEET 5 G 6 GLU A 189 VAL A 190 1 O VAL A 190 N GLY A 163 SHEET 6 G 6 PHE A 207 ILE A 208 1 O ILE A 208 N GLU A 189 SHEET 1 H 6 PHE A 116 ILE A 117 0 SHEET 2 H 6 PHE A 133 VAL A 134 1 O VAL A 134 N PHE A 116 SHEET 3 H 6 GLN A 151 ILE A 152 1 O ILE A 152 N PHE A 133 SHEET 4 H 6 ILE A 177 ILE A 178 1 O ILE A 178 N GLN A 151 SHEET 5 H 6 ILE A 195 VAL A 196 1 O VAL A 196 N ILE A 177 SHEET 6 H 6 ARG A 226 VAL A 227 1 O VAL A 227 N ILE A 195 SHEET 1 I 2 ALA B 46 ILE B 49 0 SHEET 2 I 2 GLN B 52 THR B 55 -1 O VAL B 54 N GLU B 47 SHEET 1 J 2 GLN B 73 GLU B 76 0 SHEET 2 J 2 ARG B 81 ASP B 84 -1 O TYR B 82 N MET B 75 SHEET 1 K 6 THR B 110 VAL B 111 0 SHEET 2 K 6 SER B 126 VAL B 128 1 O SER B 126 N THR B 110 SHEET 3 K 6 ALA B 144 VAL B 146 1 O VAL B 146 N TYR B 127 SHEET 4 K 6 GLY B 163 ILE B 164 1 O ILE B 164 N THR B 145 SHEET 5 K 6 GLU B 189 VAL B 190 1 O VAL B 190 N GLY B 163 SHEET 6 K 6 PHE B 207 ILE B 208 1 O ILE B 208 N GLU B 189 SHEET 1 L 6 PHE B 116 ILE B 117 0 SHEET 2 L 6 PHE B 133 VAL B 134 1 O VAL B 134 N PHE B 116 SHEET 3 L 6 GLN B 151 ILE B 152 1 O ILE B 152 N PHE B 133 SHEET 4 L 6 ILE B 177 ILE B 178 1 O ILE B 178 N GLN B 151 SHEET 5 L 6 ILE B 195 VAL B 196 1 O VAL B 196 N ILE B 177 SHEET 6 L 6 ARG B 226 VAL B 227 1 O VAL B 227 N ILE B 195 SHEET 1 M 2 ALA C 46 ILE C 49 0 SHEET 2 M 2 GLN C 52 THR C 55 -1 O GLN C 52 N ILE C 49 SHEET 1 N 2 GLN C 73 GLY C 77 0 SHEET 2 N 2 THR C 80 ASP C 84 -1 O TYR C 82 N MET C 75 SHEET 1 O 6 THR C 110 VAL C 111 0 SHEET 2 O 6 SER C 126 VAL C 128 1 O SER C 126 N THR C 110 SHEET 3 O 6 ALA C 144 VAL C 146 1 O VAL C 146 N TYR C 127 SHEET 4 O 6 GLY C 163 ILE C 164 1 O ILE C 164 N THR C 145 SHEET 5 O 6 GLU C 189 VAL C 190 1 O VAL C 190 N GLY C 163 SHEET 6 O 6 PHE C 207 ILE C 208 1 O ILE C 208 N GLU C 189 SHEET 1 P 6 PHE C 116 ILE C 117 0 SHEET 2 P 6 PHE C 133 VAL C 134 1 O VAL C 134 N PHE C 116 SHEET 3 P 6 GLN C 151 ILE C 152 1 O ILE C 152 N PHE C 133 SHEET 4 P 6 ILE C 177 ILE C 178 1 O ILE C 178 N GLN C 151 SHEET 5 P 6 ILE C 195 VAL C 196 1 O VAL C 196 N ILE C 177 SHEET 6 P 6 ARG C 226 VAL C 227 1 O VAL C 227 N ILE C 195 LINK MG MG A 275 O HOH A 346 1555 1555 2.30 LINK MG MG A 275 O HOH A 380 1555 1555 2.18 LINK MG MG A 275 O HOH B 293 1555 1555 2.04 LINK MG MG A 275 O HOH C 284 1555 1555 2.01 LINK MG MG A 275 O HOH C 317 1555 1555 2.17 CISPEP 1 PRO A 107 PRO A 108 0 4.31 CISPEP 2 GLU A 169 PRO A 170 0 1.88 CISPEP 3 PRO B 107 PRO B 108 0 1.93 CISPEP 4 GLU B 169 PRO B 170 0 -0.23 CISPEP 5 PRO C 107 PRO C 108 0 5.23 CISPEP 6 GLU C 169 PRO C 170 0 -6.94 SITE 1 AC1 5 HOH A 346 HOH A 380 HOH B 293 HOH C 284 SITE 2 AC1 5 HOH C 317 CRYST1 57.792 69.695 106.448 90.00 105.28 90.00 P 1 21 1 6 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 0.017303 0.000000 0.004727 0.00000 SCALE2 0.000000 0.014348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009739 0.00000