HEADER HYDROLASE 20-MAY-16 5K4M TITLE DIRECTED EVOLUTIONARY CHANGES IN MBL SUPER FAMILY - NDM-1 ROUND 10 TITLE 2 CRYSTAL-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-270; COMPND 5 SYNONYM: B2 METALLO-BETA-LACTAMASE,BETA-LACTAMASE TYPE II,METALLO- COMPND 6 BETA-LACTAMASE NDM-1,METALLO-BETA-LACTAMASE TYPE II,NEW DELHI COMPND 7 METALLO-BETA-LACTAMASE-1,NDM-1; COMPND 8 EC: 3.5.2.6; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PHOSPHATASE, DIRECTED EVOLUTION, MBL SUPER FAMILY, NDM-1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.-S.HONG,C.J.JACKSON,P.D.CARR REVDAT 2 27-SEP-23 5K4M 1 REMARK LINK REVDAT 1 26-APR-17 5K4M 0 JRNL AUTH F.BAIER,N.-S.HONG,G.YANG,P.D.CARR,C.JACKSON,N.TOKURIKI JRNL TITL ENZYME EVOLVABILITY IS CONTINGENT ON THE INITIAL SEQUENCE JRNL TITL 2 BACKGROUND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.98 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13877 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 736 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 993 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1410 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1699 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.29000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.155 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1843 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1722 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2510 ; 1.922 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3949 ; 0.947 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 239 ; 6.746 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;31.948 ;23.766 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 270 ;14.723 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;20.254 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 276 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2148 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 441 ; 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): 941 ; 1.637 ; 1.412 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 940 ; 1.631 ; 1.409 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1185 ; 2.747 ; 2.101 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1186 ; 2.747 ; 2.103 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 902 ; 1.894 ; 1.706 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 903 ; 1.894 ; 1.708 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1325 ; 2.957 ; 2.464 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2134 ; 6.111 ;12.797 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2135 ; 6.109 ;12.806 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 : NULL 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 5K4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 39.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02863 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.08250 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.780 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: 3SPU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.75, 1.3 M MGSO4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 39.10000 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 39.10000 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 18.91000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.08000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.91000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.08000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.10000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.91000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.08000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.10000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.91000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.08000 REMARK 290 SMTRY3 8 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 HOH A 562 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 GLY A 26 REMARK 465 HIS A 27 REMARK 465 MET A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 ILE A 31 REMARK 465 ARG A 32 REMARK 465 PRO A 33 REMARK 465 THR A 34 REMARK 465 ILE A 35 REMARK 465 GLY A 36 REMARK 465 GLN A 37 REMARK 465 GLN A 38 REMARK 465 MET A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 GLY A 42 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 OAA SV7 A 306 O HOH A 401 2.11 REMARK 500 OE2 GLU A 223 O HOH A 402 2.15 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 ARG A 264 CD ARG A 264 NE 0.105 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 A 52 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 124 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 264 CB - CG - CD ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = 5.6 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 ASP A 90 153.02 70.73 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 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD2 REMARK 620 2 HOH A 468 O 89.3 REMARK 620 3 HOH A 477 O 91.8 95.6 REMARK 620 4 HOH A 499 O 94.0 96.2 166.9 REMARK 620 5 HOH A 521 O 94.6 174.1 80.0 87.9 REMARK 620 6 HOH A 567 O 174.4 88.6 83.3 91.3 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 98.8 REMARK 620 3 HIS A 189 NE2 101.6 127.1 REMARK 620 4 SV7 A 308 OAC 116.0 107.2 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 108.0 REMARK 620 3 HIS A 250 NE2 91.3 115.2 REMARK 620 4 SV7 A 308 OAD 112.9 129.0 93.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE1 REMARK 620 2 GLU A 152 OE2 51.1 REMARK 620 3 GLU A 223 OE2 91.7 88.9 REMARK 620 4 GLU A 227 OE2 68.8 106.0 50.9 REMARK 620 5 HOH A 402 O 94.7 58.7 44.7 92.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN 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 MES A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SV7 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NPO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SV7 A 308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JQJ RELATED DB: PDB REMARK 900 RELATED ID: 5K4K RELATED DB: PDB REMARK 900 RELATED ID: 5K4N RELATED DB: PDB DBREF 5K4M A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQADV 5K4M GLY A 26 UNP C7C422 EXPRESSION TAG SEQADV 5K4M HIS A 27 UNP C7C422 EXPRESSION TAG SEQADV 5K4M MET A 28 UNP C7C422 EXPRESSION TAG SEQADV 5K4M PRO A 49 UNP C7C422 LEU 49 ENGINEERED MUTATION SEQADV 5K4M MET A 88 UNP C7C422 VAL 88 ENGINEERED MUTATION SEQADV 5K4M GLY A 93 UNP C7C422 TRP 93 ENGINEERED MUTATION SEQADV 5K4M ALA A 96 UNP C7C422 ASP 96 ENGINEERED MUTATION SEQADV 5K4M LYS A 103 UNP C7C422 ASN 103 ENGINEERED MUTATION SEQADV 5K4M ARG A 151 UNP C7C422 GLN 151 ENGINEERED MUTATION SEQADV 5K4M VAL A 154 UNP C7C422 MET 154 ENGINEERED MUTATION SEQADV 5K4M THR A 166 UNP C7C422 ASN 166 ENGINEERED MUTATION SEQADV 5K4M ARG A 211 UNP C7C422 LYS 211 ENGINEERED MUTATION SEQADV 5K4M ASP A 222 UNP C7C422 GLY 222 ENGINEERED MUTATION SEQADV 5K4M GLU A 223 UNP C7C422 ASP 223 ENGINEERED MUTATION SEQADV 5K4M VAL A 233 UNP C7C422 ALA 233 ENGINEERED MUTATION SEQADV 5K4M PHE A 251 UNP C7C422 SER 251 ENGINEERED MUTATION SEQRES 1 A 245 GLY HIS MET GLY GLU ILE ARG PRO THR ILE GLY GLN GLN SEQRES 2 A 245 MET GLU THR GLY ASP GLN ARG PHE GLY ASP PRO VAL PHE SEQRES 3 A 245 ARG GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR SEQRES 4 A 245 LEU ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY SEQRES 5 A 245 LEU ILE VAL ARG ASP GLY GLY ARG VAL LEU MET VAL ASP SEQRES 6 A 245 THR ALA GLY THR ASP ALA GLN THR ALA GLN ILE LEU LYS SEQRES 7 A 245 TRP ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA SEQRES 8 A 245 VAL VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET SEQRES 9 A 245 ASP ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN SEQRES 10 A 245 ALA LEU SER ASN GLN LEU ALA PRO ARG GLU GLY VAL VAL SEQRES 11 A 245 ALA ALA GLN HIS SER LEU THR PHE ALA ALA THR GLY TRP SEQRES 12 A 245 VAL GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS SEQRES 13 A 245 VAL PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE SEQRES 14 A 245 THR VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY SEQRES 15 A 245 CYS LEU ILE ARG ASP SER LYS ALA LYS SER LEU GLY ASN SEQRES 16 A 245 LEU ASP GLU ALA ASP THR GLU HIS TYR ALA ALA SER VAL SEQRES 17 A 245 ARG ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE SEQRES 18 A 245 VAL MET SER HIS PHE ALA PRO ASP SER ARG ALA ALA ILE SEQRES 19 A 245 THR HIS THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET MES A 303 12 HET MG A 304 1 HET MG A 305 1 HET SV7 A 306 10 HET NPO A 307 10 HET SV7 A 308 10 HETNAM ZN ZINC ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM MG MAGNESIUM ION HETNAM SV7 PHENYLPHOSPHONIC ACID HETNAM NPO P-NITROPHENOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MES C6 H13 N O4 S FORMUL 5 MG 2(MG 2+) FORMUL 7 SV7 2(C6 H7 O3 P) FORMUL 8 NPO C6 H5 N O3 FORMUL 10 HOH *187(H2 O) HELIX 1 AA1 THR A 94 ILE A 109 1 16 HELIX 2 AA2 HIS A 122 GLY A 127 1 6 HELIX 3 AA3 GLY A 128 ALA A 135 1 8 HELIX 4 AA4 ALA A 143 ALA A 149 1 7 HELIX 5 AA5 PRO A 150 GLY A 153 5 4 HELIX 6 AA6 GLU A 170 ALA A 174 5 5 HELIX 7 AA7 GLY A 207 ILE A 210 5 4 HELIX 8 AA8 HIS A 228 PHE A 240 1 13 HELIX 9 AA9 ARG A 256 LYS A 268 1 13 SHEET 1 AA1 7 VAL A 50 ALA A 55 0 SHEET 2 AA1 7 VAL A 58 ASP A 66 -1 O GLN A 60 N ARG A 52 SHEET 3 AA1 7 ALA A 72 ASP A 82 -1 O ILE A 79 N TRP A 59 SHEET 4 AA1 7 ARG A 85 VAL A 89 -1 O ARG A 85 N ASP A 82 SHEET 5 AA1 7 VAL A 113 VAL A 117 1 O ALA A 114 N VAL A 86 SHEET 6 AA1 7 ALA A 138 ASN A 142 1 O ALA A 138 N ALA A 116 SHEET 7 AA1 7 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA2 4 LEU A 180 PHE A 183 0 SHEET 2 AA2 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 AA2 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 LINK OD2 ASP A 95 MG MG A 305 1555 1555 1.93 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.10 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.02 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 1.96 LINK OE1 GLU A 152 MG MG A 304 1555 1555 2.49 LINK OE2 GLU A 152 MG MG A 304 1555 1555 2.67 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.06 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.28 LINK OE2 GLU A 223 MG MG A 304 1555 1555 3.00 LINK OE2 GLU A 227 MG MG A 304 1555 4555 2.55 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.09 LINK ZN ZN A 301 OAC SV7 A 308 1555 1555 1.97 LINK ZN ZN A 302 OAD SV7 A 308 1555 1555 1.94 LINK MG MG A 304 O HOH A 402 1555 1555 2.53 LINK MG MG A 305 O HOH A 468 1555 1555 2.12 LINK MG MG A 305 O HOH A 477 1555 1555 2.29 LINK MG MG A 305 O HOH A 499 1555 3555 2.07 LINK MG MG A 305 O HOH A 521 1555 1555 2.22 LINK MG MG A 305 O HOH A 567 1555 1555 2.02 SITE 1 AC1 4 HIS A 120 HIS A 122 HIS A 189 SV7 A 308 SITE 1 AC2 4 ASP A 124 CYS A 208 HIS A 250 SV7 A 308 SITE 1 AC3 10 VAL A 73 ARG A 85 ASN A 176 PHE A 177 SITE 2 AC3 10 GLY A 178 ARG A 211 LYS A 216 SER A 217 SITE 3 AC3 10 HIS A 250 HOH A 496 SITE 1 AC4 4 GLU A 152 GLU A 223 GLU A 227 HOH A 402 SITE 1 AC5 6 ASP A 95 HOH A 468 HOH A 477 HOH A 499 SITE 2 AC5 6 HOH A 521 HOH A 567 SITE 1 AC6 6 GLN A 53 TRP A 59 TYR A 64 ARG A 81 SITE 2 AC6 6 GLU A 108 HOH A 401 SITE 1 AC7 6 ALA A 96 ALA A 99 LEU A 102 ALA A 131 SITE 2 AC7 6 ALA A 134 ALA A 135 SITE 1 AC8 9 MET A 67 HIS A 120 HIS A 122 ASP A 124 SITE 2 AC8 9 HIS A 189 HIS A 250 ZN A 301 ZN A 302 SITE 3 AC8 9 HOH A 415 CRYST1 37.820 138.160 78.200 90.00 90.00 90.00 C 2 2 21 8 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 0.026441 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012788 0.00000