HEADER HYDROLASE 10-DEC-13 4NY5 TITLE X-RAY STRUCTURE OF THE ADDUCT FORMED BETWEEN HEN EGG WHITE LYSOZYME TITLE 2 AND NAMI-A 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: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS HYDROLASE, O-GLYCOSYL EXPDTA X-RAY DIFFRACTION AUTHOR L.MESSORI,A.MERLINO REVDAT 4 20-SEP-23 4NY5 1 REMARK LINK REVDAT 3 17-JUL-19 4NY5 1 REMARK REVDAT 2 07-MAY-14 4NY5 1 JRNL REVDAT 1 26-MAR-14 4NY5 0 JRNL AUTH L.MESSORI,A.MERLINO JRNL TITL RUTHENIUM METALATION OF PROTEINS: THE X-RAY STRUCTURE OF THE JRNL TITL 2 COMPLEX FORMED BETWEEN NAMI-A AND HEN EGG WHITE LYSOZYME. JRNL REF DALTON TRANS V. 43 6128 2014 JRNL REFN ISSN 1477-9226 JRNL PMID 24553967 JRNL DOI 10.1039/C3DT53582G REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 9628 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 490 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 683 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.91 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): 0.163 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.321 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1081 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 994 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1473 ; 1.768 ; 1.899 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2257 ; 0.961 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 140 ; 5.974 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 54 ;38.814 ;22.778 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 176 ;14.422 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.150 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 151 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1306 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 293 ; 0.002 ; 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): 545 ; 2.244 ; 2.360 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 544 ; 2.227 ; 2.356 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 690 ; 2.912 ; 3.537 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 691 ; 2.911 ; 3.542 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 536 ; 3.630 ; 2.804 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 537 ; 3.628 ; 2.808 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 784 ; 5.475 ; 4.049 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1414 ; 7.920 ;20.843 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1375 ; 7.770 ;20.511 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4NY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 22.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 4J1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF THE HEWL/NAMI-A ADDUCT REMARK 280 SUITABLE FOR X-RAY DIFFRACTION STUDIES HAVE BEEN GROWN BY REMARK 280 HANGING DROP VAPOR DIFFUSION BY MIXING 1 L OF 20 MG/ML HEWL/NAMI- REMARK 280 A COMPLEX (PROTEIN TO METAL RATIO 1:10) WITH AN EQUAL VOLUME OF REMARK 280 RESERVOIR SOLUTION CONTAINING 1.0 M NACL AND 50 MM SODIUM REMARK 280 ACETATE PH 4.5. THESE CRYSTALS WERE FISHED WITH NYLON LOOPS AND REMARK 280 FLASH-FROZEN AT 100 K USING NITROGEN GAS, WITHOUT REMARK 280 CRYOPROTECTANT. THIS PROCEDURE PARTLY DEHYDRATES THE CRYSTALS, REMARK 280 ENHANCING IN SOME CASES THE RESOLUTION OF X-RAY DIFFRACTION DATA, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 18.65800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.88600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.88600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.98700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.88600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.88600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.32900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.88600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.88600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.98700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.88600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.88600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.32900 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 18.65800 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 HOH A 305 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 356 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 401 LIES ON A SPECIAL POSITION. 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 14 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 66 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 ARG A 21 27.28 47.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE X-RAY STRUCTURE REVEALS THAT NAMI-A BINDS THE PROTEIN, AS NAKED REMARK 600 RUTHENIUM ION, AT TWO DISTINCT SITES (EITHER TO ASP101 OR TO ASP119) REMARK 600 , AFTER RELEASING ALL ITS ORIGINAL LIGANDS (DMSO, IMIDAZOLE AND CL-) REMARK 600 . THIS INDICATES THAT NAMI-A UNDERGOES DRAMATIC CHANGES IN THE REMARK 600 COORDINATION ENVIRONMENT OF THE RUTHENIUM CENTRE UPON THE PROTEIN REMARK 600 BINDING AND THAT ASP SIDE CHAINS ARE PREFERENTIAL TARGET SITES FOR REMARK 600 RUTHENIUM BINDING TO THE PROTEIN 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 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 90.3 REMARK 620 3 SER A 72 OG 87.8 163.8 REMARK 620 4 ARG A 73 O 90.0 92.9 103.2 REMARK 620 5 HOH A 354 O 102.4 88.0 76.7 167.6 REMARK 620 6 HOH A 361 O 168.7 100.9 82.0 87.6 80.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU A 202 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 HOH A 351 O 103.1 REMARK 620 3 HOH A 352 O 70.6 161.3 REMARK 620 4 HOH A 417 O 75.5 85.8 108.7 REMARK 620 5 HOH A 419 O 101.0 67.1 96.3 151.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU A 201 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 OD2 REMARK 620 2 HOH A 418 O 103.4 REMARK 620 3 HOH A 420 O 94.1 134.0 REMARK 620 4 HOH A 421 O 75.6 149.6 75.8 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 RU A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RU A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J1A RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE ADDUCT FORMED BETWEEN HEN EGG WHITE LYSOZYME REMARK 900 AND AZIRU REMARK 900 RELATED ID: 4J1B RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE ADDUCT FORMED BETWEEN HEN EGG WHITE LYSOZYME REMARK 900 AND AZIRU DBREF 4NY5 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 RU A 201 1 HET RU A 202 1 HET CL A 203 1 HET CL A 204 1 HET NA A 205 1 HETNAM RU RUTHENIUM ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 2 RU 2(RU 3+) FORMUL 4 CL 2(CL 1-) FORMUL 6 NA NA 1+ FORMUL 7 HOH *123(H2 O) HELIX 1 1 GLY A 4 HIS A 15 1 12 HELIX 2 2 ASN A 19 TYR A 23 5 5 HELIX 3 3 SER A 24 ASN A 37 1 14 HELIX 4 4 PRO A 79 SER A 85 5 7 HELIX 5 5 ILE A 88 SER A 100 1 13 HELIX 6 6 ASN A 103 ALA A 107 5 5 HELIX 7 7 TRP A 108 CYS A 115 1 8 HELIX 8 8 ASP A 119 ARG A 125 5 7 SHEET 1 A 3 THR A 43 ARG A 45 0 SHEET 2 A 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 A 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 1.99 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.06 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.07 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.06 LINK O SER A 60 NA NA A 205 1555 1555 2.25 LINK O CYS A 64 NA NA A 205 1555 1555 2.52 LINK OG SER A 72 NA NA A 205 1555 1555 2.64 LINK O ARG A 73 NA NA A 205 1555 1555 2.53 LINK OD1 ASP A 101 RU RU A 202 1555 1555 2.33 LINK OD2 ASP A 119 RU RU A 201 1555 1555 2.39 LINK RU RU A 201 O HOH A 418 1555 1555 1.86 LINK RU RU A 201 O HOH A 420 1555 1555 2.30 LINK RU RU A 201 O HOH A 421 1555 1555 2.40 LINK RU RU A 202 O HOH A 351 1555 1555 2.28 LINK RU RU A 202 O HOH A 352 1555 1555 2.62 LINK RU RU A 202 O HOH A 417 1555 1555 2.21 LINK RU RU A 202 O HOH A 419 1555 1555 1.79 LINK NA NA A 205 O HOH A 354 1555 1555 2.45 LINK NA NA A 205 O HOH A 361 1555 1555 2.47 SITE 1 AC1 5 ASP A 119 GLN A 121 HOH A 418 HOH A 420 SITE 2 AC1 5 HOH A 421 SITE 1 AC2 5 ASP A 101 HOH A 351 HOH A 352 HOH A 417 SITE 2 AC2 5 HOH A 419 SITE 1 AC3 2 TYR A 23 ASN A 113 SITE 1 AC4 6 ASN A 65 GLY A 67 ARG A 68 THR A 69 SITE 2 AC4 6 SER A 72 HOH A 354 SITE 1 AC5 6 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AC5 6 HOH A 354 HOH A 361 CRYST1 77.772 77.772 37.316 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 0.012858 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026798 0.00000