HEADER HYDROLASE 14-NOV-07 3BDH TITLE CRYSTAL STRUCTURE OF ZINC-DEFICIENT WILD-TYPE E. COLI ALKALINE TITLE 2 PHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKALINE PHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: APASE; COMPND 5 EC: 3.1.3.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PHOA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS BACTERIAL ALKALINE PHOSPHATASE, HYDROLASE, MAGNESIUM, METAL-BINDING, KEYWDS 2 PERIPLASM, PHOSPHOPROTEIN, ZINC EXPDTA X-RAY DIFFRACTION AUTHOR J.C.GRIGG,M.E.MURPHY REVDAT 3 30-AUG-23 3BDH 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 3BDH 1 VERSN REVDAT 1 18-NOV-08 3BDH 0 JRNL AUTH J.C.GRIGG,C.HUCALUK,M.E.MURPHY,H.RITTER,J.YEE,S.RAFFERTY JRNL TITL THE ACTIVE-SITE TRIMETALLIC CLUSTER OF ALKALINE PHOSPHATASE JRNL TITL 2 IS LOST UPON ISOSTERIC MUTATION AT THE MG2+-COORDINATING JRNL TITL 3 RESIDUE THREONINE-155 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0019 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 77534 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4095 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5700 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 281 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 1134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.221 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6732 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9147 ; 1.376 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 898 ; 6.890 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 279 ;40.836 ;25.842 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1094 ;14.378 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;11.646 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1045 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5122 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3614 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4652 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 903 ; 0.136 ; 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): 49 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 55 ; 0.143 ; 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): 4562 ; 0.793 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7079 ; 1.277 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2415 ; 2.255 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2068 ; 3.605 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3BDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-07 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81863 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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 1ED9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 0.2 M LISO4, 1 MM ZNCL2, 5 REMARK 280 MM MGCL2, 25-30% PEG 3350, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 51.77250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7880 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ARG A 0 REMARK 465 LEU A 450 REMARK 465 GLU A 451 REMARK 465 HIS A 452 REMARK 465 HIS A 453 REMARK 465 HIS A 454 REMARK 465 HIS A 455 REMARK 465 HIS A 456 REMARK 465 HIS A 457 REMARK 465 ARG B 0 REMARK 465 LEU B 450 REMARK 465 GLU B 451 REMARK 465 HIS B 452 REMARK 465 HIS B 453 REMARK 465 HIS B 454 REMARK 465 HIS B 455 REMARK 465 HIS B 456 REMARK 465 HIS B 457 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 327 N - CA - C ANGL. DEV. = 18.6 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 ASN A 9 97.14 -161.26 REMARK 500 ALA A 88 -164.53 -100.11 REMARK 500 SER A 238 -4.60 -140.00 REMARK 500 ASP A 327 -37.93 157.93 REMARK 500 GLN A 329 -70.23 -134.76 REMARK 500 PRO B 2 133.33 -26.36 REMARK 500 ASP B 327 23.81 -142.85 REMARK 500 GLN B 329 -124.71 62.80 REMARK 500 ASP B 408 47.98 -109.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 326 ASP A 327 -69.35 REMARK 500 ASP A 327 LYS A 328 65.99 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 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 155 OG1 REMARK 620 2 GLU A 322 OE2 87.6 REMARK 620 3 HOH A 520 O 175.3 90.5 REMARK 620 4 HOH A1032 O 91.6 94.3 84.3 REMARK 620 5 HOH A1056 O 93.9 175.1 88.4 90.3 REMARK 620 6 HOH A1059 O 94.5 87.9 89.7 173.6 87.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 155 OG1 REMARK 620 2 GLU B 322 OE2 86.2 REMARK 620 3 HOH B 508 O 92.1 88.5 REMARK 620 4 HOH B1056 O 91.9 173.0 84.8 REMARK 620 5 HOH B1065 O 174.6 91.3 92.7 91.1 REMARK 620 6 HOH B1070 O 89.0 101.6 169.9 85.1 86.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDF RELATED DB: PDB REMARK 900 RELATED ID: 3BDG RELATED DB: PDB DBREF 3BDH A 0 449 UNP P00634 PPB_ECOLI 22 471 DBREF 3BDH B 0 449 UNP P00634 PPB_ECOLI 22 471 SEQADV 3BDH LEU A 450 UNP P00634 EXPRESSION TAG SEQADV 3BDH GLU A 451 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS A 452 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS A 453 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS A 454 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS A 455 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS A 456 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS A 457 UNP P00634 EXPRESSION TAG SEQADV 3BDH LEU B 450 UNP P00634 EXPRESSION TAG SEQADV 3BDH GLU B 451 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS B 452 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS B 453 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS B 454 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS B 455 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS B 456 UNP P00634 EXPRESSION TAG SEQADV 3BDH HIS B 457 UNP P00634 EXPRESSION TAG SEQRES 1 A 458 ARG THR PRO GLU MET PRO VAL LEU GLU ASN ARG ALA ALA SEQRES 2 A 458 GLN GLY ASP ILE THR ALA PRO GLY GLY ALA ARG ARG LEU SEQRES 3 A 458 THR GLY ASP GLN THR ALA ALA LEU ARG ASP SER LEU SER SEQRES 4 A 458 ASP LYS PRO ALA LYS ASN ILE ILE LEU LEU ILE GLY ASP SEQRES 5 A 458 GLY MET GLY ASP SER GLU ILE THR ALA ALA ARG ASN TYR SEQRES 6 A 458 ALA GLU GLY ALA GLY GLY PHE PHE LYS GLY ILE ASP ALA SEQRES 7 A 458 LEU PRO LEU THR GLY GLN TYR THR HIS TYR ALA LEU ASN SEQRES 8 A 458 LYS LYS THR GLY LYS PRO ASP TYR VAL THR ASP SER ALA SEQRES 9 A 458 ALA SER ALA THR ALA TRP SER THR GLY VAL LYS THR TYR SEQRES 10 A 458 ASN GLY ALA LEU GLY VAL ASP ILE HIS GLU LYS ASP HIS SEQRES 11 A 458 PRO THR ILE LEU GLU MET ALA LYS ALA ALA GLY LEU ALA SEQRES 12 A 458 THR GLY ASN VAL SER THR ALA GLU LEU GLN ASP ALA THR SEQRES 13 A 458 PRO ALA ALA LEU VAL ALA HIS VAL THR SER ARG LYS CYS SEQRES 14 A 458 TYR GLY PRO SER ALA THR SER GLU LYS CYS PRO GLY ASN SEQRES 15 A 458 ALA LEU GLU LYS GLY GLY LYS GLY SER ILE THR GLU GLN SEQRES 16 A 458 LEU LEU ASN ALA ARG ALA ASP VAL THR LEU GLY GLY GLY SEQRES 17 A 458 ALA LYS THR PHE ALA GLU THR ALA THR ALA GLY GLU TRP SEQRES 18 A 458 GLN GLY LYS THR LEU ARG GLU GLN ALA GLN ALA ARG GLY SEQRES 19 A 458 TYR GLN LEU VAL SER ASP ALA ALA SER LEU ASN SER VAL SEQRES 20 A 458 THR GLU ALA ASN GLN GLN LYS PRO LEU LEU GLY LEU PHE SEQRES 21 A 458 ALA ASP GLY ASN MET PRO VAL ARG TRP LEU GLY PRO LYS SEQRES 22 A 458 ALA THR TYR HIS GLY ASN ILE ASP LYS PRO ALA VAL THR SEQRES 23 A 458 CYS THR PRO ASN PRO GLN ARG ASN ASP SER VAL PRO THR SEQRES 24 A 458 LEU ALA GLN MET THR ASP LYS ALA ILE GLU LEU LEU SER SEQRES 25 A 458 LYS ASN GLU LYS GLY PHE PHE LEU GLN VAL GLU GLY ALA SEQRES 26 A 458 SER ILE ASP LYS GLN ASP HIS ALA ALA ASN PRO CYS GLY SEQRES 27 A 458 GLN ILE GLY GLU THR VAL ASP LEU ASP GLU ALA VAL GLN SEQRES 28 A 458 ARG ALA LEU GLU PHE ALA LYS LYS GLU GLY ASN THR LEU SEQRES 29 A 458 VAL ILE VAL THR ALA ASP HIS ALA HIS ALA SER GLN ILE SEQRES 30 A 458 VAL ALA PRO ASP THR LYS ALA PRO GLY LEU THR GLN ALA SEQRES 31 A 458 LEU ASN THR LYS ASP GLY ALA VAL MET VAL MET SER TYR SEQRES 32 A 458 GLY ASN SER GLU GLU ASP SER GLN GLU HIS THR GLY SER SEQRES 33 A 458 GLN LEU ARG ILE ALA ALA TYR GLY PRO HIS ALA ALA ASN SEQRES 34 A 458 VAL VAL GLY LEU THR ASP GLN THR ASP LEU PHE TYR THR SEQRES 35 A 458 MET LYS ALA ALA LEU GLY LEU LYS LEU GLU HIS HIS HIS SEQRES 36 A 458 HIS HIS HIS SEQRES 1 B 458 ARG THR PRO GLU MET PRO VAL LEU GLU ASN ARG ALA ALA SEQRES 2 B 458 GLN GLY ASP ILE THR ALA PRO GLY GLY ALA ARG ARG LEU SEQRES 3 B 458 THR GLY ASP GLN THR ALA ALA LEU ARG ASP SER LEU SER SEQRES 4 B 458 ASP LYS PRO ALA LYS ASN ILE ILE LEU LEU ILE GLY ASP SEQRES 5 B 458 GLY MET GLY ASP SER GLU ILE THR ALA ALA ARG ASN TYR SEQRES 6 B 458 ALA GLU GLY ALA GLY GLY PHE PHE LYS GLY ILE ASP ALA SEQRES 7 B 458 LEU PRO LEU THR GLY GLN TYR THR HIS TYR ALA LEU ASN SEQRES 8 B 458 LYS LYS THR GLY LYS PRO ASP TYR VAL THR ASP SER ALA SEQRES 9 B 458 ALA SER ALA THR ALA TRP SER THR GLY VAL LYS THR TYR SEQRES 10 B 458 ASN GLY ALA LEU GLY VAL ASP ILE HIS GLU LYS ASP HIS SEQRES 11 B 458 PRO THR ILE LEU GLU MET ALA LYS ALA ALA GLY LEU ALA SEQRES 12 B 458 THR GLY ASN VAL SER THR ALA GLU LEU GLN ASP ALA THR SEQRES 13 B 458 PRO ALA ALA LEU VAL ALA HIS VAL THR SER ARG LYS CYS SEQRES 14 B 458 TYR GLY PRO SER ALA THR SER GLU LYS CYS PRO GLY ASN SEQRES 15 B 458 ALA LEU GLU LYS GLY GLY LYS GLY SER ILE THR GLU GLN SEQRES 16 B 458 LEU LEU ASN ALA ARG ALA ASP VAL THR LEU GLY GLY GLY SEQRES 17 B 458 ALA LYS THR PHE ALA GLU THR ALA THR ALA GLY GLU TRP SEQRES 18 B 458 GLN GLY LYS THR LEU ARG GLU GLN ALA GLN ALA ARG GLY SEQRES 19 B 458 TYR GLN LEU VAL SER ASP ALA ALA SER LEU ASN SER VAL SEQRES 20 B 458 THR GLU ALA ASN GLN GLN LYS PRO LEU LEU GLY LEU PHE SEQRES 21 B 458 ALA ASP GLY ASN MET PRO VAL ARG TRP LEU GLY PRO LYS SEQRES 22 B 458 ALA THR TYR HIS GLY ASN ILE ASP LYS PRO ALA VAL THR SEQRES 23 B 458 CYS THR PRO ASN PRO GLN ARG ASN ASP SER VAL PRO THR SEQRES 24 B 458 LEU ALA GLN MET THR ASP LYS ALA ILE GLU LEU LEU SER SEQRES 25 B 458 LYS ASN GLU LYS GLY PHE PHE LEU GLN VAL GLU GLY ALA SEQRES 26 B 458 SER ILE ASP LYS GLN ASP HIS ALA ALA ASN PRO CYS GLY SEQRES 27 B 458 GLN ILE GLY GLU THR VAL ASP LEU ASP GLU ALA VAL GLN SEQRES 28 B 458 ARG ALA LEU GLU PHE ALA LYS LYS GLU GLY ASN THR LEU SEQRES 29 B 458 VAL ILE VAL THR ALA ASP HIS ALA HIS ALA SER GLN ILE SEQRES 30 B 458 VAL ALA PRO ASP THR LYS ALA PRO GLY LEU THR GLN ALA SEQRES 31 B 458 LEU ASN THR LYS ASP GLY ALA VAL MET VAL MET SER TYR SEQRES 32 B 458 GLY ASN SER GLU GLU ASP SER GLN GLU HIS THR GLY SER SEQRES 33 B 458 GLN LEU ARG ILE ALA ALA TYR GLY PRO HIS ALA ALA ASN SEQRES 34 B 458 VAL VAL GLY LEU THR ASP GLN THR ASP LEU PHE TYR THR SEQRES 35 B 458 MET LYS ALA ALA LEU GLY LEU LYS LEU GLU HIS HIS HIS SEQRES 36 B 458 HIS HIS HIS HET MG A 501 1 HET MG B 500 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *1134(H2 O) HELIX 1 1 GLN A 29 ASP A 35 1 7 HELIX 2 2 GLY A 54 GLY A 67 1 14 HELIX 3 3 GLY A 74 LEU A 78 5 5 HELIX 4 4 ASP A 101 GLY A 112 1 12 HELIX 5 5 THR A 131 ALA A 139 1 9 HELIX 6 6 ASP A 153 ALA A 158 1 6 HELIX 7 7 GLY A 170 CYS A 178 1 9 HELIX 8 8 PRO A 179 GLY A 186 5 8 HELIX 9 9 SER A 190 ARG A 199 1 10 HELIX 10 10 ALA A 208 GLU A 213 5 6 HELIX 11 11 THR A 224 ARG A 232 1 9 HELIX 12 12 ASP A 239 VAL A 246 1 8 HELIX 13 13 HIS A 276 LYS A 281 1 6 HELIX 14 14 THR A 298 SER A 311 1 14 HELIX 15 15 ASN A 334 GLY A 360 1 27 HELIX 16 16 HIS A 425 VAL A 430 5 6 HELIX 17 17 GLN A 435 LEU A 446 1 12 HELIX 18 18 GLN B 29 SER B 36 1 8 HELIX 19 19 GLY B 54 GLY B 67 1 14 HELIX 20 20 GLY B 74 LEU B 78 5 5 HELIX 21 21 ASP B 101 GLY B 112 1 12 HELIX 22 22 THR B 131 ALA B 139 1 9 HELIX 23 23 ASP B 153 ALA B 158 1 6 HELIX 24 24 GLY B 170 CYS B 178 1 9 HELIX 25 25 PRO B 179 GLY B 186 5 8 HELIX 26 26 SER B 190 ARG B 199 1 10 HELIX 27 27 GLY B 207 GLU B 213 5 7 HELIX 28 28 THR B 224 ARG B 232 1 9 HELIX 29 29 ASP B 239 SER B 245 1 7 HELIX 30 30 HIS B 276 LYS B 281 1 6 HELIX 31 31 THR B 298 SER B 311 1 14 HELIX 32 32 LYS B 328 ALA B 332 5 5 HELIX 33 33 ASN B 334 GLY B 360 1 27 HELIX 34 34 HIS B 425 VAL B 430 5 6 HELIX 35 35 GLN B 435 LEU B 446 1 12 SHEET 1 A10 GLN A 235 VAL A 237 0 SHEET 2 A10 LEU A 255 LEU A 258 1 O LEU A 258 N VAL A 237 SHEET 3 A10 VAL A 202 GLY A 206 1 N THR A 203 O GLY A 257 SHEET 4 A10 ALA A 142 GLU A 150 1 N ALA A 149 O GLY A 206 SHEET 5 A10 PHE A 317 GLY A 323 1 O GLN A 320 N VAL A 146 SHEET 6 A10 ASN A 44 GLY A 50 1 N ILE A 49 O VAL A 321 SHEET 7 A10 THR A 362 THR A 367 1 O ILE A 365 N LEU A 48 SHEET 8 A10 LEU A 417 TYR A 422 -1 O ALA A 420 N VAL A 366 SHEET 9 A10 LEU A 80 THR A 85 -1 N TYR A 84 O LEU A 417 SHEET 10 A10 GLY A 431 ASP A 434 1 O THR A 433 N GLN A 83 SHEET 1 B 2 ALA A 88 LEU A 89 0 SHEET 2 B 2 PRO A 96 ASP A 97 -1 O ASP A 97 N ALA A 88 SHEET 1 C 2 TRP A 268 LEU A 269 0 SHEET 2 C 2 THR A 287 PRO A 288 -1 O THR A 287 N LEU A 269 SHEET 1 D 2 ALA A 371 HIS A 372 0 SHEET 2 D 2 HIS A 412 THR A 413 -1 O THR A 413 N ALA A 371 SHEET 1 E 3 GLN A 375 VAL A 377 0 SHEET 2 E 3 VAL A 397 TYR A 402 -1 O SER A 401 N GLN A 375 SHEET 3 E 3 LEU A 386 ASN A 391 -1 N LEU A 386 O TYR A 402 SHEET 1 F10 GLN B 235 VAL B 237 0 SHEET 2 F10 LEU B 255 LEU B 258 1 O LEU B 256 N GLN B 235 SHEET 3 F10 VAL B 202 GLY B 206 1 N THR B 203 O GLY B 257 SHEET 4 F10 ALA B 142 GLU B 150 1 N ALA B 149 O GLY B 206 SHEET 5 F10 PHE B 317 GLY B 323 1 O GLN B 320 N VAL B 146 SHEET 6 F10 ASN B 44 GLY B 50 1 N LEU B 47 O VAL B 321 SHEET 7 F10 THR B 362 THR B 367 1 O ILE B 365 N LEU B 48 SHEET 8 F10 LEU B 417 TYR B 422 -1 O ALA B 420 N VAL B 366 SHEET 9 F10 LEU B 80 THR B 85 -1 N GLY B 82 O ILE B 419 SHEET 10 F10 GLY B 431 ASP B 434 1 O THR B 433 N GLN B 83 SHEET 1 G 2 ALA B 88 LEU B 89 0 SHEET 2 G 2 PRO B 96 ASP B 97 -1 O ASP B 97 N ALA B 88 SHEET 1 H 2 TRP B 268 LEU B 269 0 SHEET 2 H 2 THR B 287 PRO B 288 -1 O THR B 287 N LEU B 269 SHEET 1 I 2 ALA B 371 HIS B 372 0 SHEET 2 I 2 HIS B 412 THR B 413 -1 O THR B 413 N ALA B 371 SHEET 1 J 3 GLN B 375 VAL B 377 0 SHEET 2 J 3 VAL B 397 TYR B 402 -1 O SER B 401 N GLN B 375 SHEET 3 J 3 LEU B 386 ASN B 391 -1 N LEU B 386 O TYR B 402 SSBOND 1 CYS A 168 CYS A 178 1555 1555 2.07 SSBOND 2 CYS A 286 CYS A 336 1555 1555 2.06 SSBOND 3 CYS B 168 CYS B 178 1555 1555 2.08 SSBOND 4 CYS B 286 CYS B 336 1555 1555 2.06 LINK OG1 THR A 155 MG MG A 501 1555 1555 2.13 LINK OE2 GLU A 322 MG MG A 501 1555 1555 2.10 LINK MG MG A 501 O HOH A 520 1555 1555 2.23 LINK MG MG A 501 O HOH A1032 1555 1555 2.07 LINK MG MG A 501 O HOH A1056 1555 1555 2.23 LINK MG MG A 501 O HOH A1059 1555 1555 2.05 LINK OG1 THR B 155 MG MG B 500 1555 1555 2.24 LINK OE2 GLU B 322 MG MG B 500 1555 1555 2.07 LINK MG MG B 500 O HOH B 508 1555 1555 2.12 LINK MG MG B 500 O HOH B1056 1555 1555 2.12 LINK MG MG B 500 O HOH B1065 1555 1555 2.06 LINK MG MG B 500 O HOH B1070 1555 1555 2.06 CISPEP 1 LYS A 328 GLN A 329 0 9.44 SITE 1 AC1 7 ASP B 153 THR B 155 GLU B 322 HOH B 508 SITE 2 AC1 7 HOH B1056 HOH B1065 HOH B1070 SITE 1 AC2 7 ASP A 153 THR A 155 GLU A 322 HOH A 520 SITE 2 AC2 7 HOH A1032 HOH A1056 HOH A1059 CRYST1 55.449 103.545 88.489 90.00 105.76 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 0.018035 0.000000 0.005090 0.00000 SCALE2 0.000000 0.009658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011742 0.00000