HEADER HYDROLASE 24-FEB-15 4YEM TITLE CARBOPLATIN BINDING TO HEWL IN NABR CRYSTALLISATION CONDITIONS STUDIED TITLE 2 AT AN X-RAY WAVELENGTH OF 0.9163A - NEW REFINEMENT 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 KEYWDS RE-REFINEMENT OF 4XAN, CARBOPLATIN, METAL BINDING, LYSOZYME, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.G.SHABALIN,Z.DAUTER,M.JASKOLSKI,W.MINOR,A.WLODAWER REVDAT 10 20-NOV-24 4YEM 1 REMARK REVDAT 9 27-SEP-23 4YEM 1 REMARK REVDAT 8 13-APR-22 4YEM 1 AUTHOR JRNL REVDAT 7 25-DEC-19 4YEM 1 REMARK REVDAT 6 06-SEP-17 4YEM 1 REMARK REVDAT 5 04-NOV-15 4YEM 1 JRNL REVDAT 4 30-SEP-15 4YEM 1 REMARK REVDAT 3 16-SEP-15 4YEM 1 REMARK REVDAT 2 09-SEP-15 4YEM 1 JRNL REVDAT 1 04-MAR-15 4YEM 0 JRNL AUTH I.SHABALIN,Z.DAUTER,M.JASKOLSKI,W.MINOR,A.WLODAWER JRNL TITL CRYSTALLOGRAPHY AND CHEMISTRY SHOULD ALWAYS GO TOGETHER: A JRNL TITL 2 CAUTIONARY TALE OF PROTEIN COMPLEXES WITH CISPLATIN AND JRNL TITL 3 CARBOPLATIN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 1965 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26327386 JRNL DOI 10.1107/S139900471500629X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.W.TANLEY,K.DIEDERICHS,L.M.KROON-BATENBURG,C.LEVY, REMARK 1 AUTH 2 A.M.SCHREURS,J.R.HELLIWELL REMARK 1 TITL CARBOPLATIN BINDING TO HISTIDINE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 70 1135 2014 REMARK 1 REFN ESSN 2053-230X REMARK 1 PMID 25195881 REMARK 1 DOI 10.1107/S2053230X14016161 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 17672 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) : 0.108 REMARK 3 R VALUE (WORKING SET) : 0.105 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 933 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) : 913 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.1380 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.1750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.20000 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): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.228 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 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): 1106 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1038 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1507 ; 1.494 ; 1.912 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2367 ; 1.923 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 145 ; 5.846 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;35.302 ;22.712 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 188 ;13.444 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.293 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 156 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1319 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 302 ; 0.006 ; 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): 534 ; 1.237 ; 1.090 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 532 ; 1.188 ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 669 ; 1.510 ; 1.629 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 1106 ; 1.871 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 69 ;25.729 ; 0.010 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1213 ;10.609 ; 0.010 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 REFINED INDIVIDUALLY REMARK 3 THIS DEPOSIT RESULTED FROM AN ANALYSIS OF A NUMBER OF PDB ENTRIES REMARK 3 THAT CONTAIN CISPLATIN OR CARBOPLATIN IN COMPLEX WITH PROTEINS, REMARK 3 CONDUCTED IN THE SPIRIT OF THE TERWILLIGER-BRICOGNE MOTTO REMARK 3 ADVOCATING CONTINUOUS IMPROVEMENT OF THE MACROMOLECULAR MODELS IN REMARK 3 THE PDB (ACTA CRYST. D70, 2533, 2014). THE STRUCTURE FACTORS AND REMARK 3 COORDINATES, ORIGINALLY DEPOSITED AS 4XAN (4NSF), WERE USED AS THE REMARK 3 STARTING POINT FOR AN INDEPENDENT RE-REFINEMENT. THE NEW MODEL REMARK 3 INCLUDES SOME REINTERPRETATION OF THE LIGANDS, HAS LOWER R FACTORS, REMARK 3 AND IMPROVED STATISTICS DESCRIBING THE AGREEMENT WITH THE REMARK 3 EXPERIMENTAL DATA. REMARK 4 REMARK 4 4YEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9163 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 55.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.09000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 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) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4XAN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CO-CRYSTALLIZING 20 MG ML HEWL WITH REMARK 280 1.4 MG CARBOPLATIN IN 75 ML DMSO, 462.5 ML 0.1 M SODIUM ACETATE, REMARK 280 462.5 ML 1 M NABR SOLUTION., PH 4.7, BATCH MODE, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 18.64500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.29000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.96750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.29000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.32250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.29000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.96750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.29000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.32250 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 18.64500 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 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 BR BR A 209 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 334 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 363 LIES ON A SPECIAL POSITION. 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 465 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 470 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 478 DISTANCE = 6.17 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 224 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 14 NH2 REMARK 620 2 HIS A 15 NE2 92.2 REMARK 620 3 HOH A 318 O 80.4 113.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 219 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 88.1 REMARK 620 3 SER A 72 OG 91.1 164.2 REMARK 620 4 ARG A 73 O 93.5 92.9 102.9 REMARK 620 5 HOH A 412 O 99.7 86.8 77.8 166.8 REMARK 620 6 HOH A 419 O 172.9 98.8 81.9 87.6 79.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PT A 218 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 96 NZ REMARK 620 2 HOH A 301 O 79.6 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 PT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 223 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 224 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XAN RELATED DB: PDB REMARK 900 CURRENT DEPOSIT IS INDEPENDENT RE-REFINEMENT OF 4XAN (4NSF) DBREF 4YEM A 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET PT A 201 1 HET BR A 202 1 HET BR A 203 1 HET BR A 204 1 HET BR A 205 1 HET BR A 206 1 HET BR A 207 1 HET BR A 208 1 HET BR A 209 1 HET BR A 210 2 HET BR A 211 1 HET BR A 212 1 HET BR A 213 1 HET BR A 214 1 HET BR A 215 2 HET BR A 216 1 HET BR A 217 2 HET PT A 218 1 HET NA A 219 1 HET DMS A 220 4 HET DMS A 221 4 HET ACT A 222 4 HET CL A 223 1 HET PT A 224 1 HETNAM PT PLATINUM (II) ION HETNAM BR BROMIDE ION HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION FORMUL 2 PT 3(PT 2+) FORMUL 3 BR 16(BR 1-) FORMUL 20 NA NA 1+ FORMUL 21 DMS 2(C2 H6 O S) FORMUL 23 ACT C2 H3 O2 1- FORMUL 24 CL CL 1- FORMUL 26 HOH *180(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 SER A 100 1 13 HELIX 6 AA6 ASN A 103 ALA A 107 5 5 HELIX 7 AA7 TRP A 108 CYS A 115 1 8 HELIX 8 AA8 ASP A 119 ARG A 125 5 7 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 2.02 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.06 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.06 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04 LINK NH2 ARG A 14 PT PT A 224 1555 1555 2.06 LINK ND1 HIS A 15 PT A PT A 201 1555 1555 2.13 LINK NE2 HIS A 15 PT PT A 224 1555 1555 2.65 LINK O SER A 60 NA NA A 219 1555 1555 2.33 LINK O CYS A 64 NA NA A 219 1555 1555 2.38 LINK OG SER A 72 NA NA A 219 1555 1555 2.55 LINK O ARG A 73 NA NA A 219 1555 1555 2.40 LINK NZ LYS A 96 PT PT A 218 1555 1555 2.37 LINK PT PT A 218 O HOH A 301 1555 1555 2.49 LINK NA NA A 219 O HOH A 412 1555 1555 2.49 LINK NA NA A 219 O HOH A 419 1555 1555 2.46 LINK PT PT A 224 O HOH A 318 1555 1555 2.43 SITE 1 AC1 5 HIS A 15 BR A 202 BR A 203 BR A 204 SITE 2 AC1 5 CL A 223 SITE 1 AC2 5 HIS A 15 ASN A 93 PT A 201 BR A 204 SITE 2 AC2 5 CL A 223 SITE 1 AC3 4 ARG A 14 HIS A 15 PT A 201 CL A 223 SITE 1 AC4 3 PT A 201 BR A 202 CL A 223 SITE 1 AC5 2 ILE A 88 PT A 224 SITE 1 AC6 2 TYR A 23 ASN A 113 SITE 1 AC7 3 SER A 24 GLY A 26 GLN A 121 SITE 1 AC8 2 THR A 69 SER A 72 SITE 1 AC9 2 TRP A 63 DMS A 220 SITE 1 AD1 2 PRO A 70 HOH A 324 SITE 1 AD2 2 ARG A 73 ASN A 74 SITE 1 AD3 3 LYS A 96 ARG A 128 PT A 218 SITE 1 AD4 4 ASN A 65 ASN A 74 ILE A 78 PRO A 79 SITE 1 AD5 1 ASN A 93 SITE 1 AD6 3 GLY A 4 CYS A 6 GLU A 7 SITE 1 AD7 3 LYS A 96 BR A 214 HOH A 301 SITE 1 AD8 6 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AD8 6 HOH A 412 HOH A 419 SITE 1 AD9 7 GLN A 57 ILE A 58 ASN A 59 TRP A 63 SITE 2 AD9 7 ALA A 107 TRP A 108 BR A 210 SITE 1 AE1 4 ARG A 61 TRP A 62 GLY A 71 HOH A 475 SITE 1 AE2 3 ARG A 5 TRP A 123 HOH A 364 SITE 1 AE3 4 PT A 201 BR A 202 BR A 203 BR A 204 SITE 1 AE4 4 ARG A 14 HIS A 15 BR A 205 HOH A 318 CRYST1 78.580 78.580 37.290 90.00 90.00 90.00 P 43 21 2 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 0.012726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012726 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026817 0.00000