HEADER HYDROLASE 17-JAN-16 5HMV TITLE RE REFINEMENT OF 4MWK. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 5 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 TISSUE: EGG WHITE KEYWDS STRUCTURAL DYNAMICS CISPLATIN HISTIDINE PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HELLIWELL REVDAT 9 10-JAN-24 5HMV 1 LINK REVDAT 8 01-AUG-18 5HMV 1 JRNL REVDAT 7 13-SEP-17 5HMV 1 REMARK REVDAT 6 17-AUG-16 5HMV 1 REVDAT 5 10-AUG-16 5HMV 1 JRNL REVDAT 4 27-JUL-16 5HMV 1 REVDAT 3 13-JUL-16 5HMV 1 JRNL REVDAT 2 08-JUN-16 5HMV 1 REVDAT 1 18-MAY-16 5HMV 0 SPRSDE 08-JUN-16 5HMV 4MWK JRNL AUTH S.W.TANLEY,J.R.HELLIWELL JRNL TITL COMMENT ON "STRUCTURAL DYNAMICS OF CISPLATIN BINDING TO JRNL TITL 2 HISTIDINE IN A PROTEIN" [STRUCT. DYN. 1, 034701 (2014)]. JRNL REF STRUCT DYN V. 3 37101 2016 JRNL REFN ESSN 2329-7778 JRNL PMID 27226979 JRNL DOI 10.1063/1.4948613 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.W.M.TANLEY,J.R.HELLIWELL REMARK 1 TITL STRUCTURAL DYNAMICS OF CISPLATIN BINDING TO HISTIDINE IN A REMARK 1 TITL 2 PROTEIN STRUCT. DYN. 1, 034701 (2014) REMARK 1 REF STRUCT DYN. V. 1 03471 2014 REMARK 1 REFN ESSN 2329-7778 REMARK 1 PMID 26798779 REMARK 1 DOI 10.1063/1.4883975 REMARK 2 REMARK 2 RESOLUTION. 0.98 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 48959 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) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2646 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) : 0.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2030 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.04000 REMARK 3 B13 (A**2) : 0.10000 REMARK 3 B23 (A**2) : -0.05000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.023 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.537 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1071 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1003 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1442 ; 1.975 ; 1.921 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2243 ; 0.945 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 132 ; 6.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;39.340 ;23.137 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 170 ;10.416 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;13.582 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 148 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1264 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 277 ; 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): 525 ; 0.863 ; 0.562 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 524 ; 0.862 ; 0.559 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 658 ; 1.080 ; 0.853 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 659 ; 1.079 ; 0.855 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 546 ; 2.062 ; 0.774 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 538 ; 2.061 ; 0.774 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 776 ; 2.200 ; 1.097 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1390 ; 2.291 ; 6.185 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1391 ; 2.290 ; 6.187 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2074 ; 9.813 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 27 ;13.159 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2196 ; 5.291 ; 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 5HMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217335. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL MIRROR OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48959 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 29.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.7 REMARK 200 DATA REDUNDANCY IN SHELL : 0.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 4MWK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG REMARK 280 CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR REMARK 280 EXCESS TO THE PROTEIN. 462.5 MICROL OF A 0.02M NAAC SOLUTION REMARK 280 ALONG WITH 462.5 MICROL OF A 0.5M NANO3 SOLUTION WAS USED WITH REMARK 280 75 MICROL DMSO ADDED, BATCH, PH 4.7, EVAPORATION, TEMPERATURE REMARK 280 294K, BATCH MODE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -157.0 KCAL/MOL 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 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 339 O HOH A 345 1.77 REMARK 500 O HOH A 345 O HOH A 430 1.87 REMARK 500 O HOH A 316 O HOH A 339 1.99 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 390 O HOH A 393 1645 1.90 REMARK 500 O HOH A 391 O HOH A 415 1655 2.05 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 61 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = -3.3 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 101 43.31 -95.32 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 446 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 447 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 448 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 449 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 450 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH A 453 DISTANCE = 7.34 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 7.66 ANGSTROMS REMARK 525 HOH A 455 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH A 456 DISTANCE = 8.57 ANGSTROMS 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 PT A 212 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 1 N REMARK 620 2 LYS A 1 N 7.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PT A 211 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 ND1 REMARK 620 2 HIS A 15 NE2 47.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 219 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MWK RELATED DB: PDB REMARK 900 WE ARE PROVIDING A COMMENT ARTICLE IN THE JOURNAL STRUCTURAL REMARK 900 DYNAMICS DBREF 5HMV A 1 128 UNP P00698 LYSC_CHICK 19 146 SEQRES 1 A 128 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 A 128 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 A 128 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 A 128 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 A 128 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 A 128 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 A 128 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 A 128 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 A 128 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 A 128 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG HET DMS A 201 4 HET DMS A 202 4 HET NO3 A 203 4 HET NO3 A 204 4 HET NO3 A 205 4 HET NO3 A 206 4 HET PT A 207 1 HET PT A 208 1 HET PT A 209 1 HET PT A 210 1 HET PT A 211 1 HET PT A 212 1 HET DMS A 213 4 HET NO3 A 214 4 HET NO3 A 215 4 HET NO3 A 216 4 HET CL A 217 1 HET PT A 218 1 HET CL A 219 1 HETNAM DMS DIMETHYL SULFOXIDE HETNAM NO3 NITRATE ION HETNAM PT PLATINUM (II) ION HETNAM CL CHLORIDE ION FORMUL 2 DMS 3(C2 H6 O S) FORMUL 4 NO3 7(N O3 1-) FORMUL 8 PT 7(PT 2+) FORMUL 18 CL 2(CL 1-) FORMUL 21 HOH *156(H2 O) HELIX 1 AA1 GLY A 4 HIS A 15 1 12 HELIX 2 AA2 ASN A 19 TYR A 23 5 5 HELIX 3 AA3 SER A 24 ASN A 37 1 14 HELIX 4 AA4 PRO A 79 SER A 85 5 7 HELIX 5 AA5 ILE A 88 ASP A 101 1 14 HELIX 6 AA6 GLY A 104 ALA A 107 5 4 HELIX 7 AA7 TRP A 108 CYS A 115 1 8 HELIX 8 AA8 ASP A 119 ILE A 124 5 6 SHEET 1 AA1 3 THR A 43 ARG A 45 0 SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 AA1 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.05 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.04 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04 LINK N ALYS A 1 PT PT A 212 1555 1555 2.34 LINK N BLYS A 1 PT PT A 212 1555 1555 2.21 LINK NE2 HIS A 15 PT PT A 207 1555 1555 2.13 LINK NE2 HIS A 15 PT PT A 209 1555 1555 2.53 LINK ND1 HIS A 15 PT PT A 211 1555 1555 2.76 LINK NE2 HIS A 15 PT PT A 211 1555 1555 2.58 LINK NE2 HIS A 15 PT PT A 218 1555 1555 2.41 SITE 1 AC1 8 ARG A 21 ASN A 65 ASP A 66 GLY A 67 SITE 2 AC1 8 NO3 A 215 NO3 A 216 HOH A 357 HOH A 400 SITE 1 AC2 3 ARG A 5 ALA A 122 TRP A 123 SITE 1 AC3 4 PHE A 34 LYS A 96 ARG A 114 HOH A 369 SITE 1 AC4 10 ASP A 87 THR A 89 THR A 118 ASP A 119 SITE 2 AC4 10 PT A 209 HOH A 301 HOH A 303 HOH A 304 SITE 3 AC4 10 HOH A 327 HOH A 446 SITE 1 AC5 8 TYR A 23 ARG A 45 GLY A 104 MET A 105 SITE 2 AC5 8 ASN A 106 TRP A 111 HOH A 310 HOH A 317 SITE 1 AC6 6 ASN A 46 THR A 47 ASP A 48 LYS A 97 SITE 2 AC6 6 HOH A 313 HOH A 320 SITE 1 AC7 6 HIS A 15 PT A 208 PT A 209 CL A 217 SITE 2 AC7 6 PT A 218 CL A 219 SITE 1 AC8 5 HIS A 15 PT A 207 PT A 209 CL A 217 SITE 2 AC8 5 PT A 218 SITE 1 AC9 8 HIS A 15 THR A 89 NO3 A 204 PT A 207 SITE 2 AC9 8 PT A 208 PT A 211 PT A 218 CL A 219 SITE 1 AD1 2 HIS A 15 PT A 211 SITE 1 AD2 4 HIS A 15 ASN A 37 PT A 209 PT A 210 SITE 1 AD3 3 LYS A 1 SER A 86 HOH A 371 SITE 1 AD4 6 GLN A 57 ILE A 58 ASN A 59 TRP A 63 SITE 2 AD4 6 ALA A 107 TRP A 108 SITE 1 AD5 8 SER A 24 LEU A 25 GLY A 26 GLN A 41 SITE 2 AD5 8 GLN A 121 ILE A 124 HOH A 406 HOH A 411 SITE 1 AD6 8 ASN A 65 ASN A 74 ASN A 77 ILE A 78 SITE 2 AD6 8 PRO A 79 LYS A 116 DMS A 201 HOH A 326 SITE 1 AD7 8 ARG A 21 ASP A 66 PRO A 79 CYS A 80 SITE 2 AD7 8 SER A 81 DMS A 201 HOH A 336 HOH A 350 SITE 1 AD8 6 ARG A 14 ARG A 61 PT A 207 PT A 208 SITE 2 AD8 6 PT A 218 CL A 219 SITE 1 AD9 6 HIS A 15 PT A 207 PT A 208 PT A 209 SITE 2 AD9 6 CL A 217 CL A 219 SITE 1 AE1 6 HIS A 15 ASN A 37 PT A 207 PT A 209 SITE 2 AE1 6 CL A 217 PT A 218 CRYST1 26.998 31.807 34.072 89.08 72.00 67.81 P 1 1 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 0.037040 -0.015107 -0.013851 0.00000 SCALE2 0.000000 0.033954 0.003909 0.00000 SCALE3 0.000000 0.000000 0.031063 0.00000