HEADER ISOMERASE 19-JUL-13 4LRD TITLE PHOSPHOPENTOMUTASE 4H11 VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOPENTOMUTASE 4H11 VARIANT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHODEOXYRIBOMUTASE; COMPND 5 EC: 5.4.2.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 GENE: BC_4087, DEOB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS ALKALINE PHOSPHATASE FAMILY, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.A.BIRMINGHAM,C.A.STARBIRD,T.D.PANOSIAN,D.P.NANNEMANN,T.M.IVERSON, AUTHOR 2 B.O.BACHMANN REVDAT 5 20-SEP-23 4LRD 1 REMARK SEQADV LINK REVDAT 4 30-APR-14 4LRD 1 JRNL REVDAT 3 09-APR-14 4LRD 1 JRNL REVDAT 2 26-MAR-14 4LRD 1 JRNL REVDAT 1 31-JUL-13 4LRD 0 JRNL AUTH W.R.BIRMINGHAM,C.A.STARBIRD,T.D.PANOSIAN,D.P.NANNEMANN, JRNL AUTH 2 T.M.IVERSON,B.O.BACHMANN JRNL TITL BIORETROSYNTHETIC CONSTRUCTION OF A DIDANOSINE BIOSYNTHETIC JRNL TITL 2 PATHWAY. JRNL REF NAT.CHEM.BIOL. V. 10 392 2014 JRNL REFN ISSN 1552-4450 JRNL PMID 24657930 JRNL DOI 10.1038/NCHEMBIO.1494 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 33246 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1644 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) : 1.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2331 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3071 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.27000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.007 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3168 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3013 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4280 ; 2.028 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6984 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 6.301 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;37.867 ;25.203 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 565 ;13.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.753 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3567 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 666 ; 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): 1573 ; 1.142 ; 1.136 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1571 ; 1.133 ; 1.134 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1966 ; 1.731 ; 1.698 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1967 ; 1.730 ; 1.698 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1595 ; 2.445 ; 1.453 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1595 ; 2.445 ; 1.453 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2313 ; 3.747 ; 2.064 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3748 ; 5.970 ;10.591 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3749 ; 5.969 ;10.595 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 : 1.20 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 4LRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.45 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25300 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3M8Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML PROTEIN IN 1 MM MANGANESE REMARK 280 CHLORIDE, 25 MM TRIS-HCL, PH 7.4 AGAINST A RESERVOIR OF 25% REMARK 280 PEG3350, 50 MM AMMONIUM SULFATE, 100 MM BIS-TRIS, PH 5.45, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 30.24600 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: MONOMERIC 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 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 MET A -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 LEU A -8 REMARK 465 VAL A -7 REMARK 465 PRO A -6 REMARK 465 ARG A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 REMARK 465 LYS A 393 REMARK 465 LYS A 394 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 182 CD OE1 REMARK 480 GLU A 391 OE1 OE2 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 OE1 GLU A 391 O HOH A 627 1.95 REMARK 500 O HOH A 635 O HOH A 695 2.03 REMARK 500 OD1 ASN A 2 O HOH A 651 2.05 REMARK 500 O HOH A 610 O HOH A 754 2.06 REMARK 500 O HOH A 644 O HOH A 779 2.07 REMARK 500 NZ LYS A 110 OD1 ASP A 114 2.09 REMARK 500 O2P TPO A 85 OD1 ASP A 286 2.13 REMARK 500 OE1 GLU A 391 O2 TRS A 404 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 182 CD GLU A 182 OE2 0.842 REMARK 500 GLU A 391 CD GLU A 391 OE1 0.320 REMARK 500 GLU A 391 CD GLU A 391 OE2 -0.408 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 A 98 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 LYS A 110 CB - CG - CD ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG A 193 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 230 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 294 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 338 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 PHE A 366 CB - CG - CD1 ANGL. DEV. = 4.2 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 ASP A 32 97.46 -164.57 REMARK 500 THR A 74 -168.09 -168.54 REMARK 500 ARG A 197 69.65 -119.48 REMARK 500 ASN A 205 55.73 -161.17 REMARK 500 HIS A 328 -173.07 175.04 REMARK 500 ASN A 330 78.28 -157.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 182 0.08 SIDE CHAIN REMARK 500 GLU A 391 0.07 SIDE CHAIN 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 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 13 OD2 57.8 REMARK 620 3 TPO A 85 OG1 127.3 106.9 REMARK 620 4 TPO A 85 O2P 73.5 95.7 57.1 REMARK 620 5 ASP A 327 OD2 117.7 85.6 109.8 166.7 REMARK 620 6 HIS A 328 NE2 96.9 149.9 101.6 91.5 94.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 27 O REMARK 620 2 ASP A 28 OD1 87.8 REMARK 620 3 HIS A 334 NE2 85.7 92.6 REMARK 620 4 HOH A 568 O 168.5 83.6 102.3 REMARK 620 5 HOH A 601 O 79.6 167.3 84.8 109.1 REMARK 620 6 HOH A 654 O 91.9 95.1 171.8 81.3 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPO A 85 O3P REMARK 620 2 TPO A 85 O2P 59.1 REMARK 620 3 ASP A 286 OD1 105.2 50.6 REMARK 620 4 HIS A 291 NE2 156.6 143.9 95.2 REMARK 620 5 HIS A 339 NE2 84.4 86.0 111.1 98.9 REMARK 620 6 HOH A 502 O 78.9 98.9 88.8 90.5 156.9 REMARK 620 7 HOH A 503 O 71.3 130.1 164.1 86.0 84.3 75.3 REMARK 620 8 HOH A 519 O 15.9 46.9 89.8 163.9 93.6 74.3 85.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UN3 RELATED DB: PDB REMARK 900 RELATED ID: 3TX0 RELATED DB: PDB REMARK 900 RELATED ID: 3TWZ RELATED DB: PDB REMARK 900 RELATED ID: 3M8Z RELATED DB: PDB REMARK 900 RELATED ID: 4LR7 RELATED DB: PDB REMARK 900 RELATED ID: 4LR8 RELATED DB: PDB REMARK 900 RELATED ID: 4LR9 RELATED DB: PDB REMARK 900 RELATED ID: 4LRA RELATED DB: PDB REMARK 900 RELATED ID: 4LRB RELATED DB: PDB REMARK 900 RELATED ID: 4LRC RELATED DB: PDB REMARK 900 RELATED ID: 4LRE RELATED DB: PDB REMARK 900 RELATED ID: 4LRF RELATED DB: PDB DBREF 4LRD A 2 394 UNP Q818Z9 DEOB_BACCR 2 394 SEQADV 4LRD MET A -21 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD GLY A -20 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD SER A -19 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD SER A -18 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -17 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -16 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -15 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -14 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -13 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -12 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD SER A -11 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD SER A -10 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD GLY A -9 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD LEU A -8 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD VAL A -7 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD PRO A -6 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD ARG A -5 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD GLY A -4 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD SER A -3 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD HIS A -2 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD MET A -1 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD ALA A 0 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD SER A 1 UNP Q818Z9 EXPRESSION TAG SEQADV 4LRD ILE A 81 UNP Q818Z9 THR 81 ENGINEERED MUTATION SEQADV 4LRD LEU A 158 UNP Q818Z9 VAL 158 ENGINEERED MUTATION SEQADV 4LRD LYS A 190 UNP Q818Z9 MET 190 ENGINEERED MUTATION SEQRES 1 A 416 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 416 LEU VAL PRO ARG GLY SER HIS MET ALA SER ASN LYS TYR SEQRES 3 A 416 LYS ARG ILE PHE LEU VAL VAL MET ASP SER VAL GLY ILE SEQRES 4 A 416 GLY GLU ALA PRO ASP ALA GLU GLN PHE GLY ASP LEU GLY SEQRES 5 A 416 SER ASP THR ILE GLY HIS ILE ALA GLU HIS MET ASN GLY SEQRES 6 A 416 LEU GLN MET PRO ASN MET VAL LYS LEU GLY LEU GLY ASN SEQRES 7 A 416 ILE ARG GLU MET LYS GLY ILE SER LYS VAL GLU LYS PRO SEQRES 8 A 416 LEU GLY TYR TYR THR LYS MET GLN GLU LYS SER ILE GLY SEQRES 9 A 416 LYS ASP TPO MET THR GLY HIS TRP GLU ILE MET GLY LEU SEQRES 10 A 416 TYR ILE ASP THR PRO PHE GLN VAL PHE PRO GLU GLY PHE SEQRES 11 A 416 PRO LYS GLU LEU LEU ASP GLU LEU GLU GLU LYS THR GLY SEQRES 12 A 416 ARG LYS ILE ILE GLY ASN LYS PRO ALA SER GLY THR GLU SEQRES 13 A 416 ILE LEU ASP GLU LEU GLY GLN GLU GLN MET GLU THR GLY SEQRES 14 A 416 SER LEU ILE VAL TYR THR SER ALA ASP SER LEU LEU GLN SEQRES 15 A 416 ILE ALA ALA HIS GLU GLU VAL VAL PRO LEU ASP GLU LEU SEQRES 16 A 416 TYR LYS ILE CYS LYS ILE ALA ARG GLU LEU THR LEU ASP SEQRES 17 A 416 GLU LYS TYR LYS VAL GLY ARG VAL ILE ALA ARG PRO PHE SEQRES 18 A 416 VAL GLY GLU PRO GLY ASN PHE THR ARG THR PRO ASN ARG SEQRES 19 A 416 HIS ASP TYR ALA LEU LYS PRO PHE GLY ARG THR VAL MET SEQRES 20 A 416 ASN GLU LEU LYS ASP SER ASP TYR ASP VAL ILE ALA ILE SEQRES 21 A 416 GLY LYS ILE SER ASP ILE TYR ASP GLY GLU GLY VAL THR SEQRES 22 A 416 GLU SER LEU ARG THR LYS SER ASN MET ASP GLY MET ASP SEQRES 23 A 416 LYS LEU VAL ASP THR LEU ASN MET ASP PHE THR GLY LEU SEQRES 24 A 416 SER PHE LEU ASN LEU VAL ASP PHE ASP ALA LEU PHE GLY SEQRES 25 A 416 HIS ARG ARG ASP PRO GLN GLY TYR GLY GLU ALA LEU GLN SEQRES 26 A 416 GLU TYR ASP ALA ARG LEU PRO GLU VAL PHE ALA LYS LEU SEQRES 27 A 416 LYS GLU ASP ASP LEU LEU LEU ILE THR ALA ASP HIS GLY SEQRES 28 A 416 ASN ASP PRO ILE HIS PRO GLY THR ASP HIS THR ARG GLU SEQRES 29 A 416 TYR VAL PRO LEU LEU ALA TYR SER PRO SER MET LYS GLU SEQRES 30 A 416 GLY GLY GLN GLU LEU PRO LEU ARG GLN THR PHE ALA ASP SEQRES 31 A 416 ILE GLY ALA THR VAL ALA GLU ASN PHE GLY VAL LYS MET SEQRES 32 A 416 PRO GLU TYR GLY THR SER PHE LEU ASN GLU LEU LYS LYS MODRES 4LRD TPO A 85 THR PHOSPHOTHREONINE HET TPO A 85 11 HET MN A 401 1 HET MN A 402 1 HET MN A 403 1 HET TRS A 404 8 HET GOL A 405 6 HET GOL A 406 6 HETNAM TPO PHOSPHOTHREONINE HETNAM MN MANGANESE (II) ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETSYN TPO PHOSPHONOTHREONINE HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 TPO C4 H10 N O6 P FORMUL 2 MN 3(MN 2+) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *305(H2 O) HELIX 1 1 ALA A 23 GLY A 27 5 5 HELIX 2 2 ASP A 32 MET A 41 1 10 HELIX 3 3 MET A 46 GLY A 53 1 8 HELIX 4 4 GLY A 53 ARG A 58 1 6 HELIX 5 5 ASP A 84 MET A 93 1 10 HELIX 6 6 PRO A 109 GLY A 121 1 13 HELIX 7 7 SER A 131 GLY A 147 1 17 HELIX 8 8 PRO A 169 THR A 184 1 16 HELIX 9 9 LEU A 185 LYS A 190 5 6 HELIX 10 10 THR A 223 SER A 231 1 9 HELIX 11 11 LYS A 240 TYR A 245 1 6 HELIX 12 12 SER A 258 ASN A 271 1 14 HELIX 13 13 VAL A 283 PHE A 289 1 7 HELIX 14 14 ASP A 294 LEU A 316 1 23 HELIX 15 15 PHE A 366 GLY A 378 1 13 HELIX 16 16 PHE A 388 LEU A 392 5 5 SHEET 1 A 7 TYR A 72 MET A 76 0 SHEET 2 A 7 VAL A 344 TYR A 349 -1 O ALA A 348 N TYR A 72 SHEET 3 A 7 ASP A 320 THR A 325 -1 N LEU A 322 O TYR A 349 SHEET 4 A 7 ARG A 6 MET A 12 1 N PHE A 8 O LEU A 323 SHEET 5 A 7 GLY A 276 LEU A 282 1 O LEU A 280 N LEU A 9 SHEET 6 A 7 ASP A 234 ILE A 238 1 N ILE A 238 O PHE A 279 SHEET 7 A 7 GLU A 252 LEU A 254 1 O LEU A 254 N ALA A 237 SHEET 1 B 5 ILE A 124 PRO A 129 0 SHEET 2 B 5 LEU A 149 THR A 153 1 O LEU A 149 N ILE A 125 SHEET 3 B 5 LEU A 158 HIS A 164 -1 O GLN A 160 N TYR A 152 SHEET 4 B 5 ARG A 193 GLU A 202 1 O ARG A 197 N ILE A 161 SHEET 5 B 5 ASN A 205 ARG A 208 -1 O THR A 207 N VAL A 200 SHEET 1 C 5 ILE A 124 PRO A 129 0 SHEET 2 C 5 LEU A 149 THR A 153 1 O LEU A 149 N ILE A 125 SHEET 3 C 5 LEU A 158 HIS A 164 -1 O GLN A 160 N TYR A 152 SHEET 4 C 5 ARG A 193 GLU A 202 1 O ARG A 197 N ILE A 161 SHEET 5 C 5 HIS A 213 ALA A 216 -1 O HIS A 213 N ALA A 196 LINK C ASP A 84 N TPO A 85 1555 1555 1.32 LINK C TPO A 85 N MET A 86 1555 1555 1.35 LINK OD1 ASP A 13 MN MN A 402 1555 1555 2.09 LINK OD2 ASP A 13 MN MN A 402 1555 1555 2.51 LINK O GLY A 27 MN MN A 403 1555 1555 2.41 LINK OD1 ASP A 28 MN MN A 403 1555 1555 2.15 LINK O3PATPO A 85 MN MN A 401 1555 1555 2.01 LINK O2PATPO A 85 MN MN A 401 1555 1555 2.72 LINK OG1 TPO A 85 MN MN A 402 1555 1555 2.07 LINK O2PATPO A 85 MN MN A 402 1555 1555 2.65 LINK OD1 ASP A 286 MN MN A 401 1555 1555 2.10 LINK NE2 HIS A 291 MN MN A 401 1555 1555 2.21 LINK OD2 ASP A 327 MN MN A 402 1555 1555 2.07 LINK NE2 HIS A 328 MN MN A 402 1555 1555 2.16 LINK NE2 HIS A 334 MN MN A 403 1555 1555 2.49 LINK NE2 HIS A 339 MN MN A 401 1555 1555 2.19 LINK MN MN A 401 O HOH A 502 1555 1555 2.24 LINK MN MN A 401 O HOH A 503 1555 1555 2.28 LINK MN MN A 401 O BHOH A 519 1555 1555 2.32 LINK MN MN A 403 O HOH A 568 1555 1555 2.30 LINK MN MN A 403 O HOH A 601 1555 1555 2.30 LINK MN MN A 403 O HOH A 654 1555 1555 2.24 SITE 1 AC1 7 TPO A 85 ASP A 286 HIS A 291 HIS A 339 SITE 2 AC1 7 HOH A 502 HOH A 503 HOH A 519 SITE 1 AC2 4 ASP A 13 TPO A 85 ASP A 327 HIS A 328 SITE 1 AC3 6 GLY A 27 ASP A 28 HIS A 334 HOH A 568 SITE 2 AC3 6 HOH A 601 HOH A 654 SITE 1 AC4 6 GLU A 300 GLN A 303 ASN A 390 GLU A 391 SITE 2 AC4 6 HOH A 647 HOH A 751 SITE 1 AC5 9 ASP A 284 LEU A 288 GLU A 375 ASN A 390 SITE 2 AC5 9 HOH A 509 HOH A 546 HOH A 564 HOH A 594 SITE 3 AC5 9 HOH A 605 SITE 1 AC6 3 GLY A 30 ASP A 32 HIS A 36 CRYST1 39.293 60.492 78.854 90.00 98.50 90.00 P 1 21 1 2 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 0.025450 0.000000 0.003801 0.00000 SCALE2 0.000000 0.016531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012822 0.00000