HEADER TRANSPORT PROTEIN 28-APR-14 4Q8R TITLE CRYSTAL STRUCTURE OF A PHOSPHATE BINDING PROTEIN (PBP-1) FROM TITLE 2 CLOSTRIDIUM PERFRINGENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATE ABC TRANSPORTER, PHOSPHATE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-276; COMPND 5 SYNONYM: HIGH AFFINITY PHOSPHATE BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 GENE: PSTS, CPF_0617; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PERIPLASMIC HIGH AFFINITY PHOSPHATE BINDING PROTEIN, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.GONZALEZ,M.RICHEZ,C.BERGONZI,E.CHABRIERE,M.ELIAS REVDAT 2 20-SEP-23 4Q8R 1 REMARK SEQADV LINK REVDAT 1 05-NOV-14 4Q8R 0 JRNL AUTH D.GONZALEZ,M.RICHEZ,C.BERGONZI,E.CHABRIERE,M.ELIAS JRNL TITL CRYSTAL STRUCTURE OF THE PHOSPHATE-BINDING PROTEIN (PBP-1) JRNL TITL 2 OF AN ABC-TYPE PHOSPHATE TRANSPORTER FROM CLOSTRIDIUM JRNL TITL 3 PERFRINGENS. JRNL REF SCI REP V. 4 6636 2014 JRNL REFN ESSN 2045-2322 JRNL PMID 25338617 JRNL DOI 10.1038/SREP06636 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31475 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) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1657 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2293 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1818 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 196 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : -1.30000 REMARK 3 B33 (A**2) : 0.70000 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): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.961 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1933 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1890 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2631 ; 1.944 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4408 ; 2.903 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 5.861 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;35.826 ;27.073 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 370 ;13.665 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;12.460 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 308 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2218 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 378 ; 0.013 ; 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): 993 ; 3.270 ; 2.947 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 992 ; 3.287 ; 2.944 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1247 ; 3.778 ; 4.429 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1248 ; 3.782 ; 4.432 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 940 ; 5.313 ; 3.444 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 937 ; 5.322 ; 3.450 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1364 ; 5.951 ; 4.975 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2317 ; 6.227 ;25.210 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2239 ; 5.549 ;24.432 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3823 ; 8.864 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 75 ;42.001 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3912 ;20.836 ; 5.000 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 4Q8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33131 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 37.564 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 4GD5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60 MG/ML PROTEIN, 0.1 N SODIUM REMARK 280 ACETATE, PH 4.5, 0.2 M ZINC ACETATE, 10% PEG3000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.86500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.22500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.86500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.22500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.86500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.22500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.86500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.22500 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 73.22500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 73.22500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 73.22500 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 73.22500 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.86500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 52.86500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 52.86500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 35.39000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 52.86500 REMARK 290 SMTRY3 16 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 ZN ZN A 303 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 408 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 506 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 572 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 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 A 541 O HOH A 556 1.77 REMARK 500 O HOH A 534 O HOH A 545 1.79 REMARK 500 OD2 ASP A 127 O HOH A 541 1.85 REMARK 500 O HOH A 550 O HOH A 557 1.86 REMARK 500 OE2 GLU A 137 O HOH A 531 1.88 REMARK 500 O HOH A 420 O HOH A 508 1.95 REMARK 500 OE1 GLU A 137 O HOH A 420 1.96 REMARK 500 O HOH A 548 O HOH A 593 1.97 REMARK 500 O HOH A 479 O HOH A 507 2.00 REMARK 500 O HOH A 567 O HOH A 586 2.05 REMARK 500 O HOH A 533 O HOH A 544 2.07 REMARK 500 OE2 GLU A 240 O HOH A 567 2.08 REMARK 500 OE1 GLN A 164 O HOH A 532 2.09 REMARK 500 O HOH A 504 O HOH A 548 2.10 REMARK 500 O HOH A 498 O HOH A 508 2.10 REMARK 500 O HOH A 456 O HOH A 549 2.11 REMARK 500 OD1 ASP A 133 O HOH A 420 2.13 REMARK 500 OE2 GLU A 75 O HOH A 558 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 583 O HOH A 583 11655 1.93 REMARK 500 NZ LYS A 106 O HOH A 451 14545 1.95 REMARK 500 O HOH A 532 O HOH A 533 2655 2.07 REMARK 500 O HOH A 431 O HOH A 559 2655 2.18 REMARK 500 O HOH A 466 O HOH A 466 11655 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 SER A 5 CB SER A 5 OG 0.113 REMARK 500 GLU A 65 CB GLU A 65 CG -0.118 REMARK 500 GLU A 144 CD GLU A 144 OE1 0.089 REMARK 500 SER A 223 CB SER A 223 OG -0.097 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 188 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES 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 ZN A 305 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 61 OD1 REMARK 620 2 GLU A 73 OE2 93.0 REMARK 620 3 GLU A 73 OE2 93.5 35.2 REMARK 620 4 GLU A 73 OE1 143.3 58.9 49.8 REMARK 620 5 HOH A 550 O 82.3 130.8 96.0 98.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 86 NE2 REMARK 620 2 HOH A 551 O 115.5 REMARK 620 3 HOH A 552 O 83.7 80.1 REMARK 620 4 HOH A 566 O 102.1 95.4 173.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 231 OE2 REMARK 620 2 GLU A 231 OE2 11.8 REMARK 620 3 ASP A 235 OD2 117.1 108.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GD5 RELATED DB: PDB REMARK 900 PHOSPHATE BINDING PROTEIN (PBP-1) FROM CLOSTRIDIUM PERFRINGENS, P21 REMARK 900 SPACE GROUP DBREF 4Q8R A 1 246 UNP Q0TTH0 Q0TTH0_CLOP1 31 276 SEQADV 4Q8R HIS A 247 UNP Q0TTH0 EXPRESSION TAG SEQADV 4Q8R HIS A 248 UNP Q0TTH0 EXPRESSION TAG SEQADV 4Q8R HIS A 249 UNP Q0TTH0 EXPRESSION TAG SEQADV 4Q8R HIS A 250 UNP Q0TTH0 EXPRESSION TAG SEQADV 4Q8R HIS A 251 UNP Q0TTH0 EXPRESSION TAG SEQADV 4Q8R HIS A 252 UNP Q0TTH0 EXPRESSION TAG SEQRES 1 A 252 LYS SER THR ASN SER VAL SER ILE SER GLY SER THR SER SEQRES 2 A 252 VAL GLY PRO VAL MET GLU ALA GLU ALA GLU ALA PHE LYS SEQRES 3 A 252 THR LYS LYS PRO ASP VAL SER ILE GLU ILE ASN GLN ILE SEQRES 4 A 252 GLY SER SER ALA GLY ILE LYS ASN ALA MET GLU GLY VAL SEQRES 5 A 252 SER GLU ILE GLY MET ALA SER ARG ASP LEU LYS GLY GLU SEQRES 6 A 252 GLU LYS GLN ALA GLY LEU LYS GLU VAL GLU ILE ALA TYR SEQRES 7 A 252 ASP GLY ILE ALA LEU ILE THR HIS LYS ASN ASN PRO VAL SEQRES 8 A 252 LYS ASP LEU THR LEU VAL GLN ILE LYS ASP ILE TYR THR SEQRES 9 A 252 GLY LYS ILE THR ASN TRP LYS GLU LEU GLY GLY ASN ASP SEQRES 10 A 252 ALA PRO ILE VAL VAL VAL SER ARG GLU ASP GLY SER GLY SEQRES 11 A 252 THR ARG ASP ALA PHE GLN GLU ILE VAL GLY PHE LYS ALA SEQRES 12 A 252 GLU GLU LEU THR VAL ASN SER GLN ILE SER ASP GLY SER SEQRES 13 A 252 GLY ASN ILE LYS SER LEU VAL GLN GLY ASN GLU ASN ALA SEQRES 14 A 252 ILE GLY TYR ILE SER PHE SER TYR VAL ASP ASP SER VAL SEQRES 15 A 252 SER ALA VAL LYS VAL ASP GLY VAL GLU ALA THR PRO GLU SEQRES 16 A 252 ASN VAL LEU ASN LYS SER TYR LYS VAL SER ARG PRO PHE SEQRES 17 A 252 LEU ALA VAL TYR LYS GLU GLU ASN LEU THR GLU SER GLY SEQRES 18 A 252 LYS SER PHE ILE ASP PHE ILE LEU SER GLU GLU GLY GLN SEQRES 19 A 252 ASP ILE VAL ALA LYS GLU HIS LEU ILE LYS VAL LYS HIS SEQRES 20 A 252 HIS HIS HIS HIS HIS HET PO4 A 301 5 HET ZN A 302 1 HET ZN A 303 1 HET ZN A 304 1 HET ZN A 305 1 HETNAM PO4 PHOSPHATE ION HETNAM ZN ZINC ION FORMUL 2 PO4 O4 P 3- FORMUL 3 ZN 4(ZN 2+) FORMUL 7 HOH *196(H2 O) HELIX 1 1 VAL A 14 LYS A 29 1 16 HELIX 2 2 GLY A 40 GLU A 50 1 11 HELIX 3 3 LYS A 63 ALA A 69 1 7 HELIX 4 4 THR A 95 THR A 104 1 10 HELIX 5 5 ASN A 109 GLY A 114 5 6 HELIX 6 6 SER A 129 GLY A 140 1 12 HELIX 7 7 LYS A 142 LEU A 146 5 5 HELIX 8 8 GLY A 155 GLY A 165 1 11 HELIX 9 9 SER A 176 VAL A 178 5 3 HELIX 10 10 THR A 193 ASN A 199 1 7 HELIX 11 11 THR A 218 SER A 230 1 13 HELIX 12 12 SER A 230 GLU A 240 1 11 SHEET 1 A 8 ILE A 34 GLN A 38 0 SHEET 2 A 8 VAL A 6 GLY A 10 1 N VAL A 6 O GLU A 35 SHEET 3 A 8 ILE A 55 ALA A 58 1 O MET A 57 N SER A 9 SHEET 4 A 8 SER A 205 TYR A 212 -1 O LEU A 209 N ALA A 58 SHEET 5 A 8 LYS A 72 HIS A 86 -1 N LYS A 72 O TYR A 212 SHEET 6 A 8 ALA A 169 SER A 174 -1 O ILE A 173 N ALA A 82 SHEET 7 A 8 VAL A 121 ARG A 125 1 N VAL A 123 O ILE A 170 SHEET 8 A 8 GLN A 151 SER A 153 1 O GLN A 151 N VAL A 122 SHEET 1 B 6 ILE A 34 GLN A 38 0 SHEET 2 B 6 VAL A 6 GLY A 10 1 N VAL A 6 O GLU A 35 SHEET 3 B 6 ILE A 55 ALA A 58 1 O MET A 57 N SER A 9 SHEET 4 B 6 SER A 205 TYR A 212 -1 O LEU A 209 N ALA A 58 SHEET 5 B 6 LYS A 72 HIS A 86 -1 N LYS A 72 O TYR A 212 SHEET 6 B 6 VAL A 182 ALA A 184 -1 O SER A 183 N THR A 85 SHEET 1 C 2 ASP A 93 LEU A 94 0 SHEET 2 C 2 LYS A 186 VAL A 187 1 O LYS A 186 N LEU A 94 LINK OD1 ASP A 61 ZN ZN A 305 1555 1555 2.02 LINK OE2BGLU A 73 ZN ZN A 305 1555 1555 1.83 LINK OE2AGLU A 73 ZN ZN A 305 1555 1555 2.19 LINK OE1BGLU A 73 ZN ZN A 305 1555 1555 2.46 LINK NE2 HIS A 86 ZN ZN A 304 1555 1555 2.07 LINK OE2BGLU A 231 ZN ZN A 303 1555 1555 1.85 LINK OE2AGLU A 231 ZN ZN A 303 1555 1555 2.01 LINK OD2 ASP A 235 ZN ZN A 303 1555 1555 2.04 LINK NE2 HIS A 241 ZN ZN A 302 1555 1555 2.32 LINK ZN ZN A 304 O HOH A 551 1555 1555 1.97 LINK ZN ZN A 304 O HOH A 552 1555 1555 2.69 LINK ZN ZN A 304 O HOH A 566 1555 1555 2.19 LINK ZN ZN A 305 O HOH A 550 1555 1555 1.76 SITE 1 AC1 10 SER A 11 THR A 12 SER A 13 GLY A 40 SITE 2 AC1 10 SER A 41 SER A 59 ARG A 125 SER A 129 SITE 3 AC1 10 GLY A 130 THR A 131 SITE 1 AC2 2 HIS A 241 HOH A 518 SITE 1 AC3 2 GLU A 231 ASP A 235 SITE 1 AC4 5 GLU A 23 HIS A 86 HOH A 551 HOH A 552 SITE 2 AC4 5 HOH A 566 SITE 1 AC5 4 ASP A 61 GLU A 73 HOH A 550 HOH A 557 CRYST1 70.780 105.730 146.450 90.00 90.00 90.00 F 2 2 2 16 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 0.014128 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006828 0.00000