HEADER HYDROLASE 03-FEB-17 5N0I TITLE CRYSTAL STRUCTURE OF NDM-1 IN COMPLEX WITH BETA-MERCAPTOETHANOL - NEW TITLE 2 REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A, B; 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 BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS HYDROLASE, NDM-1, METALLO-BETA-LACTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.RACZYNSKA,I.G.SHABALIN,M.JASKOLSKI,W.MINOR,A.WLODAWER,D.T.KING, AUTHOR 2 N.C.J.STRYNADKA REVDAT 2 26-DEC-18 5N0I 1 JRNL REVDAT 1 05-APR-17 5N0I 0 JRNL AUTH J.E.RACZYNSKA,I.G.SHABALIN,W.MINOR,A.WLODAWER,M.JASKOLSKI JRNL TITL A CLOSE LOOK ONTO STRUCTURAL MODELS AND PRIMARY LIGANDS OF JRNL TITL 2 METALLO-BETA-LACTAMASES. JRNL REF DRUG RESIST. UPDAT. V. 40 1 2018 JRNL REFN ESSN 1532-2084 JRNL PMID 30466711 JRNL DOI 10.1016/J.DRUP.2018.08.001 REMARK 0 REMARK 0 THIS ENTRY 5N0I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA (R4EXYSF) DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 4EXY: D.T.KING, N.C.J.STRYNADKA ORIGINAL DATA REFERENCE 1 PDB ID: REMARK 0 4EXY AUTH D.T.KING,L.J.WORRALL,R.GRUNINGER,N.C.STRYNADKA TITL REMARK 0 NEW DELHI METALLO-BETA-LACTAMASE: STRUCTURAL INSIGHTS INTO TITL REMARK 0 2 BETA-LACTAM RECOGNITION AND INHIBITION REF J.AM.CHEM.SOC. V. REMARK 0 134 11362 2012 REFN ISSN 0002-7863 PMID 22713171 DOI 10.1021/ REMARK 0 JA303579D REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 87106 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : COPIED FROM 4EXY REMARK 3 R VALUE (WORKING + TEST SET) : 0.111 REMARK 3 R VALUE (WORKING SET) : 0.110 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4592 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6170 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 327 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3497 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.40000 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): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.827 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3731 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3502 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5094 ; 1.648 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8058 ; 1.046 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 504 ; 5.849 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;33.301 ;24.813 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 567 ;12.187 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;20.634 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 578 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4338 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 842 ; 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): 1920 ; 3.113 ; 1.497 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1919 ; 3.058 ; 1.496 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2405 ; 3.918 ; 2.255 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2406 ; 3.936 ; 2.256 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1811 ; 4.297 ; 1.849 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1811 ; 4.296 ; 1.849 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2673 ; 4.789 ; 2.605 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4603 ; 5.937 ;14.893 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4604 ; 5.937 ;60.633 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7224 ; 2.170 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 166 ;34.801 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7525 ;12.061 ; 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 : 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 5N0I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : TEROIDAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 35.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37200 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG8K, 8% W/V ETHYLENE GLYCOL, REMARK 280 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 46.42500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.61000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.21250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.61000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.61000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.63750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.61000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.61000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.21250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.61000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.61000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.63750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.42500 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLY B 29 REMARK 465 GLU B 30 REMARK 465 ILE B 31 REMARK 465 ARG B 32 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO B 33 CG CD REMARK 470 ILE B 35 CG1 CG2 CD1 REMARK 470 PHE B 70 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN B 220 CG OD1 ND2 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 85 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET A 126 CG - SD - CE ANGL. DEV. = 10.5 DEGREES REMARK 500 ASP B 124 CB - CG - OD1 ANGL. DEV. = 5.5 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 82 75.37 -110.81 REMARK 500 ASP A 90 140.93 76.06 REMARK 500 PRO B 68 116.88 -36.35 REMARK 500 ASP B 90 142.93 76.05 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 A 686 DISTANCE = 5.98 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 B 306 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 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 99.5 REMARK 620 3 HIS A 189 NE2 100.8 111.8 REMARK 620 4 BME A 303 S2 135.7 110.4 97.6 REMARK 620 N 1 2 3 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 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 111.2 REMARK 620 3 HIS A 250 NE2 90.9 107.1 REMARK 620 4 BME A 303 S2 111.1 116.7 117.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 98.9 REMARK 620 3 HIS B 189 NE2 101.6 112.9 REMARK 620 4 BME B 303 S2 135.4 110.0 97.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 110.4 REMARK 620 3 HIS B 250 NE2 91.8 107.2 REMARK 620 4 BME B 303 S2 112.1 116.0 116.8 REMARK 620 N 1 2 3 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 BME A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EXY RELATED DB: PDB REMARK 900 RE-REFINEMENT OF ENTRY 4EXY DBREF 5N0I A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 DBREF 5N0I B 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQADV 5N0I LYS A 271 UNP C7C422 EXPRESSION TAG SEQADV 5N0I LEU A 272 UNP C7C422 EXPRESSION TAG SEQADV 5N0I LYS B 271 UNP C7C422 EXPRESSION TAG SEQADV 5N0I LEU B 272 UNP C7C422 EXPRESSION TAG SEQRES 1 A 244 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 A 244 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 A 244 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 A 244 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 A 244 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 A 244 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 A 244 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 A 244 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 A 244 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 A 244 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 A 244 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 A 244 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 A 244 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 A 244 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 A 244 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 A 244 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 A 244 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 A 244 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 A 244 ALA ARG MET ALA ASP LYS LEU ARG LYS LEU SEQRES 1 B 244 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 B 244 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 B 244 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 B 244 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 B 244 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 B 244 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 B 244 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 B 244 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 B 244 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 B 244 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 B 244 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 B 244 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 B 244 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 B 244 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 B 244 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 B 244 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 B 244 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 B 244 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 B 244 ALA ARG MET ALA ASP LYS LEU ARG LYS LEU HET ZN A 301 1 HET ZN A 302 1 HET BME A 303 4 HET GOL A 304 6 HET GOL A 305 6 HET ZN B 301 1 HET ZN B 302 1 HET BME B 303 4 HET GOL B 304 6 HET CL B 305 1 HET PG4 B 306 5 HETNAM ZN ZINC ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 BME 2(C2 H6 O S) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 12 CL CL 1- FORMUL 13 PG4 C8 H18 O5 FORMUL 14 HOH *568(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 GLY A 153 1 11 HELIX 5 AA5 GLU A 170 ALA A 174 5 5 HELIX 6 AA6 GLY A 207 ILE A 210 5 4 HELIX 7 AA7 HIS A 228 PHE A 240 1 13 HELIX 8 AA8 ARG A 256 LEU A 272 1 17 HELIX 9 AA9 THR B 94 ILE B 109 1 16 HELIX 10 AB1 HIS B 122 GLY B 127 1 6 HELIX 11 AB2 GLY B 128 ALA B 135 1 8 HELIX 12 AB3 ALA B 143 GLY B 153 1 11 HELIX 13 AB4 GLU B 170 ALA B 174 5 5 HELIX 14 AB5 HIS B 228 PHE B 240 1 13 HELIX 15 AB6 ARG B 256 LYS B 271 1 16 SHEET 1 AA1 8 ASP A 43 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 AA1 8 VAL A 58 TYR A 64 -1 O GLN A 60 N ARG A 52 SHEET 4 AA1 8 ALA A 74 ASP A 82 -1 O ILE A 79 N TRP A 59 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 AA1 8 VAL A 113 VAL A 117 1 O VAL A 117 N VAL A 88 SHEET 7 AA1 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA1 8 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 SHEET 1 AA3 9 GLN B 37 GLN B 38 0 SHEET 2 AA3 9 GLN B 44 PHE B 46 -1 O ARG B 45 N GLN B 37 SHEET 3 AA3 9 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 4 AA3 9 VAL B 58 MET B 67 -1 O GLN B 60 N ARG B 52 SHEET 5 AA3 9 GLY B 71 ASP B 82 -1 O VAL B 73 N LEU B 65 SHEET 6 AA3 9 ARG B 85 VAL B 89 -1 O ARG B 85 N ASP B 82 SHEET 7 AA3 9 VAL B 113 VAL B 118 1 O ALA B 114 N VAL B 86 SHEET 8 AA3 9 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 9 AA3 9 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 AA4 4 LEU B 180 PHE B 183 0 SHEET 2 AA4 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 AA4 4 ILE B 203 PHE B 205 -1 O PHE B 205 N VAL B 196 SHEET 4 AA4 4 MET B 245 VAL B 247 1 O VAL B 247 N ALA B 204 LINK NE2 HIS A 120 ZN ZN A 302 1555 1555 2.02 LINK ND1 HIS A 122 ZN ZN A 302 1555 1555 2.00 LINK OD2 ASP A 124 ZN ZN A 301 1555 1555 1.99 LINK NE2 HIS A 189 ZN ZN A 302 1555 1555 2.03 LINK SG CYS A 208 ZN ZN A 301 1555 1555 2.27 LINK NE2 HIS A 250 ZN ZN A 301 1555 1555 2.04 LINK NE2 HIS B 120 ZN ZN B 302 1555 1555 2.01 LINK ND1 HIS B 122 ZN ZN B 302 1555 1555 2.03 LINK OD2 ASP B 124 ZN ZN B 301 1555 1555 1.99 LINK NE2 HIS B 189 ZN ZN B 302 1555 1555 2.04 LINK SG CYS B 208 ZN ZN B 301 1555 1555 2.27 LINK NE2 HIS B 250 ZN ZN B 301 1555 1555 2.05 LINK ZN ZN A 301 S2 BME A 303 1555 1555 2.30 LINK ZN ZN A 302 S2 BME A 303 1555 1555 2.29 LINK ZN ZN B 301 S2 BME B 303 1555 1555 2.30 LINK ZN ZN B 302 S2 BME B 303 1555 1555 2.28 SITE 1 AC1 5 ASP A 124 CYS A 208 HIS A 250 ZN A 302 SITE 2 AC1 5 BME A 303 SITE 1 AC2 5 HIS A 120 HIS A 122 HIS A 189 ZN A 301 SITE 2 AC2 5 BME A 303 SITE 1 AC3 7 HIS A 122 ASP A 124 HIS A 189 ASN A 220 SITE 2 AC3 7 ZN A 301 ZN A 302 HOH A 529 SITE 1 AC4 7 ARG A 81 ILE A 109 HOH A 419 HOH A 425 SITE 2 AC4 7 ARG B 52 GLN B 53 LEU B 54 SITE 1 AC5 7 LYS A 106 ASN A 110 LEU A 111 HOH A 431 SITE 2 AC5 7 HOH A 521 GLU B 40 THR B 41 SITE 1 AC6 5 ASP B 124 CYS B 208 HIS B 250 ZN B 302 SITE 2 AC6 5 BME B 303 SITE 1 AC7 5 HIS B 120 HIS B 122 HIS B 189 ZN B 301 SITE 2 AC7 5 BME B 303 SITE 1 AC8 7 HIS B 122 ASP B 124 HIS B 189 ZN B 301 SITE 2 AC8 7 ZN B 302 GOL B 304 HOH B 532 SITE 1 AC9 8 HIS B 122 GLY B 219 ASN B 220 LEU B 221 SITE 2 AC9 8 BME B 303 HOH B 401 HOH B 408 HOH B 491 SITE 1 AD1 5 PHE B 240 PRO B 241 LYS B 242 ALA B 243 SITE 2 AD1 5 HOH B 613 SITE 1 AD2 4 LEU B 65 ASP B 66 HOH B 500 HOH B 583 CRYST1 107.220 107.220 92.850 90.00 90.00 90.00 P 41 21 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 0.009327 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010770 0.00000