HEADER HYDROLASE 01-MAY-08 3D0K TITLE CRYSTAL STRUCTURE OF THE LPQC, POLY(3-HYDROXYBUTYRATE) DEPOLYMERASE TITLE 2 FROM BORDETELLA PARAPERTUSSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE POLY(3-HYDROXYBUTYRATE) DEPOLYMERASE LPQC; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORDETELLA PARAPERTUSSIS 12822; SOURCE 3 ORGANISM_TAXID: 257311; SOURCE 4 STRAIN: 12822 / NCTC 13253; SOURCE 5 ATCC: BAA-587; SOURCE 6 GENE: BPP4128; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19B KEYWDS ALPHA-BETA-ALPHA SANDWICH, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,C.TESAR,R.JEDRZEJCZAK,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 3 13-JUL-11 3D0K 1 VERSN REVDAT 2 24-FEB-09 3D0K 1 VERSN REVDAT 1 01-JUL-08 3D0K 0 JRNL AUTH Y.KIM,C.TESAR,R.JEDRZEJCZAK,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF THE LPQC, POLY(3-HYDROXYBUTYRATE) JRNL TITL 2 DEPOLYMERASE FROM BORDETELLA PARAPERTUSSIS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 52230 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2803 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) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3773 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 214 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 439 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 20.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : 1.35000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.264 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4853 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6643 ; 1.639 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 599 ; 6.211 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 250 ;35.634 ;22.360 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 667 ;15.257 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;19.518 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 675 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3920 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2397 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3262 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 416 ; 0.162 ; 0.200 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): 58 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.182 ; 0.200 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): 3035 ; 1.077 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4738 ; 1.705 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2074 ; 3.075 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1905 ; 4.704 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 296 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7433 30.1432 92.8531 REMARK 3 T TENSOR REMARK 3 T11: -0.0599 T22: -0.0403 REMARK 3 T33: -0.0289 T12: 0.0137 REMARK 3 T13: -0.0100 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.5706 L22: 0.6383 REMARK 3 L33: 1.2958 L12: 0.1083 REMARK 3 L13: 0.3970 L23: 0.3952 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.0272 S13: -0.0049 REMARK 3 S21: 0.0170 S22: -0.0198 S23: -0.0233 REMARK 3 S31: -0.0016 S32: -0.0702 S33: 0.0123 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 296 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3231 33.9353 42.2585 REMARK 3 T TENSOR REMARK 3 T11: -0.0404 T22: -0.0551 REMARK 3 T33: -0.0286 T12: -0.0074 REMARK 3 T13: 0.0110 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 0.5549 L22: 0.5327 REMARK 3 L33: 0.9334 L12: -0.0642 REMARK 3 L13: 0.2626 L23: -0.1936 REMARK 3 S TENSOR REMARK 3 S11: -0.0238 S12: -0.0040 S13: -0.0163 REMARK 3 S21: -0.0269 S22: 0.0276 S23: -0.0307 REMARK 3 S31: 0.0014 S32: 0.0066 S33: -0.0038 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: NULL REMARK 4 REMARK 4 3D0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB047439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-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) : 0.97920 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54978 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 41.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12000 REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.59800 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000, MLPHARE, DM, SHELXD, RESOLVE, COOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M MES PH REMARK 280 6.5, 10% DIOXANE, 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 41.85500 REMARK 290 SMTRY3 2 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 300 REMARK: AUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL REMARK 300 UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE. 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 MSE A 1 REMARK 465 LYS A 2 REMARK 465 PRO A 3 REMARK 465 ALA A 4 REMARK 465 ASP A 29 REMARK 465 ASP A 30 REMARK 465 ARG A 31 REMARK 465 ASP A 217 REMARK 465 ASP A 218 REMARK 465 GLY A 297 REMARK 465 SER A 298 REMARK 465 GLN A 299 REMARK 465 SER A 300 REMARK 465 ALA A 301 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MSE B 1 REMARK 465 ASP B 217 REMARK 465 ASP B 218 REMARK 465 GLY B 297 REMARK 465 SER B 298 REMARK 465 GLN B 299 REMARK 465 SER B 300 REMARK 465 ALA B 301 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 O HOH B 356 O HOH B 357 2.08 REMARK 500 O HOH B 464 O HOH B 556 2.13 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 ARG B 153 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 153 NE - CZ - NH2 ANGL. DEV. = -3.7 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 LYS A 79 61.06 60.20 REMARK 500 TYR A 98 -80.52 -104.63 REMARK 500 SER A 145 -123.32 60.15 REMARK 500 ASP B 30 -73.32 -67.15 REMARK 500 ASN B 32 42.22 -143.83 REMARK 500 TYR B 98 -78.13 -104.63 REMARK 500 SER B 145 -121.96 60.56 REMARK 500 ASN B 170 48.62 39.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 425 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH B 428 DISTANCE = 5.63 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC60195 RELATED DB: TARGETDB DBREF 3D0K A 1 301 UNP Q7W3B7 Q7W3B7_BORPA 1 301 DBREF 3D0K B 1 301 UNP Q7W3B7 Q7W3B7_BORPA 1 301 SEQADV 3D0K SER A -2 UNP Q7W3B7 EXPRESSION TAG SEQADV 3D0K ASN A -1 UNP Q7W3B7 EXPRESSION TAG SEQADV 3D0K ALA A 0 UNP Q7W3B7 EXPRESSION TAG SEQADV 3D0K SER B -2 UNP Q7W3B7 EXPRESSION TAG SEQADV 3D0K ASN B -1 UNP Q7W3B7 EXPRESSION TAG SEQADV 3D0K ALA B 0 UNP Q7W3B7 EXPRESSION TAG SEQRES 1 A 304 SER ASN ALA MSE LYS PRO ALA ASP LEU THR ASN ALA ASP SEQRES 2 A 304 ARG ILE ALA LEU GLU LEU GLY HIS ALA GLY ARG ASN ALA SEQRES 3 A 304 ILE PRO TYR LEU ASP ASP ASP ARG ASN ALA ASP ARG PRO SEQRES 4 A 304 PHE THR LEU ASN THR TYR ARG PRO TYR GLY TYR THR PRO SEQRES 5 A 304 ASP ARG PRO VAL VAL VAL VAL GLN HIS GLY VAL LEU ARG SEQRES 6 A 304 ASN GLY ALA ASP TYR ARG ASP PHE TRP ILE PRO ALA ALA SEQRES 7 A 304 ASP ARG HIS LYS LEU LEU ILE VAL ALA PRO THR PHE SER SEQRES 8 A 304 ASP GLU ILE TRP PRO GLY VAL GLU SER TYR ASN ASN GLY SEQRES 9 A 304 ARG ALA PHE THR ALA ALA GLY ASN PRO ARG HIS VAL ASP SEQRES 10 A 304 GLY TRP THR TYR ALA LEU VAL ALA ARG VAL LEU ALA ASN SEQRES 11 A 304 ILE ARG ALA ALA GLU ILE ALA ASP CYS GLU GLN VAL TYR SEQRES 12 A 304 LEU PHE GLY HIS SER ALA GLY GLY GLN PHE VAL HIS ARG SEQRES 13 A 304 LEU MSE SER SER GLN PRO HIS ALA PRO PHE HIS ALA VAL SEQRES 14 A 304 THR ALA ALA ASN PRO GLY TRP TYR THR LEU PRO THR PHE SEQRES 15 A 304 GLU HIS ARG PHE PRO GLU GLY LEU ASP GLY VAL GLY LEU SEQRES 16 A 304 THR GLU ASP HIS LEU ALA ARG LEU LEU ALA TYR PRO MSE SEQRES 17 A 304 THR ILE LEU ALA GLY ASP GLN ASP ILE ALA THR ASP ASP SEQRES 18 A 304 PRO ASN LEU PRO SER GLU PRO ALA ALA LEU ARG GLN GLY SEQRES 19 A 304 PRO HIS ARG TYR ALA ARG ALA ARG HIS TYR TYR GLU ALA SEQRES 20 A 304 GLY GLN ARG ALA ALA ALA GLN ARG GLY LEU PRO PHE GLY SEQRES 21 A 304 TRP GLN LEU GLN VAL VAL PRO GLY ILE GLY HIS ASP GLY SEQRES 22 A 304 GLN ALA MSE SER GLN VAL CYS ALA SER LEU TRP PHE ASP SEQRES 23 A 304 GLY ARG MSE PRO ASP ALA ALA GLU LEU ALA ARG LEU ALA SEQRES 24 A 304 GLY SER GLN SER ALA SEQRES 1 B 304 SER ASN ALA MSE LYS PRO ALA ASP LEU THR ASN ALA ASP SEQRES 2 B 304 ARG ILE ALA LEU GLU LEU GLY HIS ALA GLY ARG ASN ALA SEQRES 3 B 304 ILE PRO TYR LEU ASP ASP ASP ARG ASN ALA ASP ARG PRO SEQRES 4 B 304 PHE THR LEU ASN THR TYR ARG PRO TYR GLY TYR THR PRO SEQRES 5 B 304 ASP ARG PRO VAL VAL VAL VAL GLN HIS GLY VAL LEU ARG SEQRES 6 B 304 ASN GLY ALA ASP TYR ARG ASP PHE TRP ILE PRO ALA ALA SEQRES 7 B 304 ASP ARG HIS LYS LEU LEU ILE VAL ALA PRO THR PHE SER SEQRES 8 B 304 ASP GLU ILE TRP PRO GLY VAL GLU SER TYR ASN ASN GLY SEQRES 9 B 304 ARG ALA PHE THR ALA ALA GLY ASN PRO ARG HIS VAL ASP SEQRES 10 B 304 GLY TRP THR TYR ALA LEU VAL ALA ARG VAL LEU ALA ASN SEQRES 11 B 304 ILE ARG ALA ALA GLU ILE ALA ASP CYS GLU GLN VAL TYR SEQRES 12 B 304 LEU PHE GLY HIS SER ALA GLY GLY GLN PHE VAL HIS ARG SEQRES 13 B 304 LEU MSE SER SER GLN PRO HIS ALA PRO PHE HIS ALA VAL SEQRES 14 B 304 THR ALA ALA ASN PRO GLY TRP TYR THR LEU PRO THR PHE SEQRES 15 B 304 GLU HIS ARG PHE PRO GLU GLY LEU ASP GLY VAL GLY LEU SEQRES 16 B 304 THR GLU ASP HIS LEU ALA ARG LEU LEU ALA TYR PRO MSE SEQRES 17 B 304 THR ILE LEU ALA GLY ASP GLN ASP ILE ALA THR ASP ASP SEQRES 18 B 304 PRO ASN LEU PRO SER GLU PRO ALA ALA LEU ARG GLN GLY SEQRES 19 B 304 PRO HIS ARG TYR ALA ARG ALA ARG HIS TYR TYR GLU ALA SEQRES 20 B 304 GLY GLN ARG ALA ALA ALA GLN ARG GLY LEU PRO PHE GLY SEQRES 21 B 304 TRP GLN LEU GLN VAL VAL PRO GLY ILE GLY HIS ASP GLY SEQRES 22 B 304 GLN ALA MSE SER GLN VAL CYS ALA SER LEU TRP PHE ASP SEQRES 23 B 304 GLY ARG MSE PRO ASP ALA ALA GLU LEU ALA ARG LEU ALA SEQRES 24 B 304 GLY SER GLN SER ALA MODRES 3D0K MSE A 155 MET SELENOMETHIONINE MODRES 3D0K MSE A 205 MET SELENOMETHIONINE MODRES 3D0K MSE A 273 MET SELENOMETHIONINE MODRES 3D0K MSE A 286 MET SELENOMETHIONINE MODRES 3D0K MSE B 155 MET SELENOMETHIONINE MODRES 3D0K MSE B 205 MET SELENOMETHIONINE MODRES 3D0K MSE B 273 MET SELENOMETHIONINE MODRES 3D0K MSE B 286 MET SELENOMETHIONINE HET MSE A 155 8 HET MSE A 205 8 HET MSE A 273 8 HET MSE A 286 8 HET MSE B 155 8 HET MSE B 205 8 HET MSE B 273 8 HET MSE B 286 8 HET CL A 302 1 HET CL A 303 1 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 A 306 5 HET SO4 A 307 5 HET SO4 A 308 5 HET SO4 A 309 5 HET CL B 302 1 HET SO4 B 303 5 HET SO4 B 304 5 HET SO4 B 305 5 HET SO4 B 306 5 HET SO4 B 307 5 HET SO4 B 308 5 HET FMT A 310 3 HET FMT B 309 3 HET FMT B 310 3 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM FMT FORMIC ACID FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 CL 3(CL 1-) FORMUL 5 SO4 12(O4 S 2-) FORMUL 18 FMT 3(C H2 O2) FORMUL 21 HOH *439(H2 O) HELIX 1 1 THR A 7 LEU A 16 1 10 HELIX 2 2 ASN A 63 TRP A 71 1 9 HELIX 3 3 TRP A 71 LYS A 79 1 9 HELIX 4 4 PRO A 93 TYR A 98 1 6 HELIX 5 5 HIS A 112 TYR A 118 5 7 HELIX 6 6 ALA A 119 ALA A 131 1 13 HELIX 7 7 SER A 145 GLN A 158 1 14 HELIX 8 8 THR A 193 TYR A 203 1 11 HELIX 9 9 GLU A 224 ARG A 229 1 6 HELIX 10 10 HIS A 233 ARG A 252 1 20 HELIX 11 11 ASP A 269 ASP A 283 1 15 HELIX 12 12 ASP A 288 ALA A 296 1 9 HELIX 13 13 LYS B 2 LEU B 6 5 5 HELIX 14 14 THR B 7 LEU B 16 1 10 HELIX 15 15 ASN B 63 TRP B 71 1 9 HELIX 16 16 TRP B 71 LYS B 79 1 9 HELIX 17 17 PRO B 93 TYR B 98 1 6 HELIX 18 18 HIS B 112 TYR B 118 5 7 HELIX 19 19 ALA B 119 ALA B 131 1 13 HELIX 20 20 SER B 145 GLN B 158 1 14 HELIX 21 21 THR B 193 TYR B 203 1 11 HELIX 22 22 GLU B 224 ARG B 229 1 6 HELIX 23 23 HIS B 233 ARG B 252 1 20 HELIX 24 24 ASP B 269 ASP B 283 1 15 HELIX 25 25 ASP B 288 ALA B 296 1 9 SHEET 1 A 8 GLY A 20 TYR A 26 0 SHEET 2 A 8 PHE A 37 ARG A 43 -1 O PHE A 37 N TYR A 26 SHEET 3 A 8 LEU A 81 THR A 86 -1 O THR A 86 N THR A 38 SHEET 4 A 8 VAL A 53 GLN A 57 1 N VAL A 54 O LEU A 81 SHEET 5 A 8 VAL A 139 HIS A 144 1 O TYR A 140 N VAL A 55 SHEET 6 A 8 ALA A 165 ALA A 169 1 O ALA A 169 N GLY A 143 SHEET 7 A 8 THR A 206 GLY A 210 1 O LEU A 208 N ALA A 168 SHEET 8 A 8 GLN A 259 VAL A 263 1 O GLN A 261 N ILE A 207 SHEET 1 B 8 GLY B 20 TYR B 26 0 SHEET 2 B 8 PHE B 37 ARG B 43 -1 O ARG B 43 N GLY B 20 SHEET 3 B 8 LEU B 81 THR B 86 -1 O THR B 86 N THR B 38 SHEET 4 B 8 VAL B 53 GLN B 57 1 N VAL B 54 O LEU B 81 SHEET 5 B 8 VAL B 139 HIS B 144 1 O TYR B 140 N VAL B 55 SHEET 6 B 8 ALA B 165 ALA B 169 1 O ALA B 169 N GLY B 143 SHEET 7 B 8 THR B 206 GLY B 210 1 O LEU B 208 N ALA B 168 SHEET 8 B 8 GLN B 259 VAL B 263 1 O GLN B 259 N ILE B 207 LINK C LEU A 154 N MSE A 155 1555 1555 1.32 LINK C MSE A 155 N SER A 156 1555 1555 1.34 LINK C PRO A 204 N MSE A 205 1555 1555 1.32 LINK C MSE A 205 N THR A 206 1555 1555 1.35 LINK C ALA A 272 N MSE A 273 1555 1555 1.34 LINK C MSE A 273 N SER A 274 1555 1555 1.33 LINK C ARG A 285 N MSE A 286 1555 1555 1.32 LINK C MSE A 286 N PRO A 287 1555 1555 1.35 LINK C LEU B 154 N MSE B 155 1555 1555 1.34 LINK C MSE B 155 N SER B 156 1555 1555 1.35 LINK C PRO B 204 N MSE B 205 1555 1555 1.32 LINK C MSE B 205 N THR B 206 1555 1555 1.34 LINK C ALA B 272 N MSE B 273 1555 1555 1.33 LINK C MSE B 273 N SER B 274 1555 1555 1.34 LINK C ARG B 285 N MSE B 286 1555 1555 1.33 LINK C MSE B 286 N PRO B 287 1555 1555 1.35 CISPEP 1 PHE A 183 PRO A 184 0 7.84 CISPEP 2 PHE B 183 PRO B 184 0 2.37 SITE 1 AC1 1 ARG B 111 SITE 1 AC2 6 SER A 145 ALA A 146 GLN A 149 GLY A 172 SITE 2 AC2 6 PRO A 222 ARG A 234 SITE 1 AC3 7 SER B 145 ALA B 146 GLN B 149 GLY B 172 SITE 2 AC3 7 ASN B 220 PRO B 222 ARG B 234 SITE 1 AC4 5 GLY B 59 TYR B 67 HIS B 144 SER B 145 SITE 2 AC4 5 HIS B 268 SITE 1 AC5 3 THR A 105 ALA A 107 ASN A 109 SITE 1 AC6 2 TYR B 45 GLY B 46 SITE 1 AC7 5 GLY A 59 TYR A 67 HIS A 144 SER A 145 SITE 2 AC7 5 HIS A 268 SITE 1 AC8 4 ARG A 21 SER B 88 ASP B 89 GLU B 90 SITE 1 AC9 3 ASP B 188 GLY B 189 GLY B 191 SITE 1 BC1 4 GLY B 94 GLU B 96 ARG B 285 ASP B 288 SITE 1 BC2 3 HIS A 18 ALA A 19 TYR A 45 SITE 1 BC3 3 GLY A 94 GLU A 96 ARG A 285 SITE 1 BC4 2 ASP A 288 ALA A 289 SITE 1 BC5 4 ASN A 63 GLY A 64 ALA A 65 ASP A 66 SITE 1 BC6 4 ASN B 63 GLY B 64 ALA B 65 ASP B 66 SITE 1 BC7 3 ALA B 33 ASP B 34 ARG B 35 CRYST1 41.879 83.710 90.792 90.00 92.68 90.00 P 1 21 1 4 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 0.023878 0.000000 0.001119 0.00000 SCALE2 0.000000 0.011946 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011026 0.00000