HEADER HYDROLASE 27-AUG-14 4W94 TITLE CRYSTAL STRUCTURE OF CROSS-LINKED TETRAGONAL HEN EGG WHITE LYSOZYME TITLE 2 SOAKED WITH 5MM [RU(CO)3CL2]2 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 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.TABE,K.FUJITA,S.ABE,M.TSUJIMOTO,T.KUCHIMARU,S.KIZAKA-KONDO, AUTHOR 2 M.TAKANO,S.KITAGAWA,T.UENO REVDAT 4 08-NOV-23 4W94 1 LINK REVDAT 3 29-JAN-20 4W94 1 SOURCE JRNL REMARK REVDAT 2 14-JAN-15 4W94 1 JRNL REVDAT 1 31-DEC-14 4W94 0 JRNL AUTH H.TABE,K.FUJITA,S.ABE,M.TSUJIMOTO,T.KUCHIMARU, JRNL AUTH 2 S.KIZAKA-KONDOH,M.TAKANO,S.KITAGAWA,T.UENO JRNL TITL PREPARATION OF A CROSS-LINKED POROUS PROTEIN CRYSTAL JRNL TITL 2 CONTAINING RU CARBONYL COMPLEXES AS A CO-RELEASING JRNL TITL 3 EXTRACELLULAR SCAFFOLD JRNL REF INORG.CHEM. V. 54 215 2015 JRNL REFN ISSN 0020-1669 JRNL PMID 25494847 JRNL DOI 10.1021/IC502159X REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 16476 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 877 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1197 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 995 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.532 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1047 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1415 ; 2.218 ; 1.910 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 132 ; 6.305 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;40.407 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 165 ;14.817 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;15.154 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 146 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 809 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 645 ; 1.503 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1022 ; 2.504 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 402 ; 3.642 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 391 ; 5.724 ; 4.500 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): 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 : 1.40 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4W94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALEPACK, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 58.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 193L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, SODIUM ACETATE, PH 4.5, VAPOR REMARK 280 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 18.46000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.51700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.51700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.69000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.51700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.51700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.23000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.51700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.51700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.69000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.51700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.51700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.23000 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 18.46000 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 RU RU A 219 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 307 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 364 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 367 LIES ON A SPECIAL POSITION. 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 ARG A 125 CG CD NE CZ NH1 NH2 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 OD2 ASP A 52 O HOH A 410 2.11 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 ASP A 52 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 61 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES 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 RU A 220 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 13 NZ REMARK 620 2 HOH A 330 O 76.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU1 A 206 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 RU1 A 206 C1 169.5 REMARK 620 3 RU1 A 206 C2 90.0 87.4 REMARK 620 4 HOH A 301 O 90.4 93.1 175.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU1 A 209 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 18 OD1 REMARK 620 2 RU1 A 209 C1 80.8 REMARK 620 3 RU1 A 209 C2 168.0 87.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU1 A 212 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 18 OD2 REMARK 620 2 RU1 A 212 C1 171.0 REMARK 620 3 RU1 A 212 C2 83.7 87.4 REMARK 620 4 HOH A 330 O 89.2 92.5 91.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU A 214 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 52 OD2 REMARK 620 2 HOH A 398 O 112.4 REMARK 620 3 HOH A 399 O 91.8 104.0 REMARK 620 4 HOH A 410 O 48.3 160.6 81.4 REMARK 620 N 1 2 3 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 89.6 REMARK 620 3 SER A 72 OG 87.0 168.1 REMARK 620 4 ARG A 73 O 94.6 91.4 100.3 REMARK 620 5 HOH A 382 O 169.2 100.5 82.4 89.2 REMARK 620 6 HOH A 383 O 97.9 86.9 82.3 167.4 78.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU A 219 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 129 O REMARK 620 2 LEU A 129 O 0.0 REMARK 620 3 HOH A 364 O 143.1 143.1 REMARK 620 4 HOH A 364 O 139.8 139.8 5.4 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 DMF A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU1 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU1 A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU1 A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RU A 220 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4W96 RELATED DB: PDB DBREF 4W94 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 DMF A 201 5 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET NA A 205 1 HET RU1 A 206 5 HET CL A 207 1 HET CL A 208 1 HET RU1 A 209 5 HET CL A 210 1 HET CL A 211 1 HET RU1 A 212 5 HET CL A 213 1 HET RU A 214 1 HET RU A 215 1 HET RU A 216 1 HET RU A 217 1 HET CL A 218 1 HET RU A 219 1 HET RU A 220 1 HETNAM DMF DIMETHYLFORMAMIDE HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM RU1 BIS(OXIDANIUMYLIDYNEMETHYL)RUTHENIUM(2+) HETNAM RU RUTHENIUM ION FORMUL 2 DMF C3 H7 N O FORMUL 3 CL 9(CL 1-) FORMUL 6 NA NA 1+ FORMUL 7 RU1 3(C2 O2 RU 4+) FORMUL 15 RU 6(RU 3+) FORMUL 22 HOH *110(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 2.01 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.07 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 LINK NZ LYS A 13 RU RU A 220 1555 1555 1.82 LINK NE2 HIS A 15 RU RU1 A 206 1555 1555 2.33 LINK OD1 ASP A 18 RU RU1 A 209 1555 1555 2.12 LINK OD2 ASP A 18 RU RU1 A 212 1555 1555 2.12 LINK OD2 ASP A 52 RU RU A 214 1555 1555 2.73 LINK O SER A 60 NA NA A 205 1555 1555 2.31 LINK O CYS A 64 NA NA A 205 1555 1555 2.44 LINK OG SER A 72 NA NA A 205 1555 1555 2.58 LINK O ARG A 73 NA NA A 205 1555 1555 2.36 LINK OD1 ASP A 101 RU RU A 215 1555 1555 2.35 LINK OD2 ASP A 101 RU RU A 216 1555 1555 2.26 LINK OD2 ASP A 119 RU RU A 217 1555 1555 2.37 LINK O LEU A 129 RU RU A 219 1555 1555 2.61 LINK O LEU A 129 RU RU A 219 1555 7555 2.61 LINK NA NA A 205 O HOH A 382 1555 1555 2.43 LINK NA NA A 205 O HOH A 383 1555 1555 2.35 LINK RU RU1 A 206 O HOH A 301 1555 1555 2.00 LINK RU RU1 A 212 O HOH A 330 1555 1555 2.62 LINK RU RU A 214 O HOH A 398 1555 1555 2.00 LINK RU RU A 214 O HOH A 399 1555 1555 2.49 LINK RU RU A 214 O HOH A 410 1555 1555 2.37 LINK RU RU A 219 O HOH A 364 1555 1555 2.07 LINK RU RU A 219 O HOH A 364 1555 7555 2.07 LINK RU RU A 220 O HOH A 330 1555 1555 2.65 SITE 1 AC1 9 GLN A 57 ILE A 58 ASN A 59 TRP A 63 SITE 2 AC1 9 ALA A 107 TRP A 108 RU A 214 HOH A 380 SITE 3 AC1 9 HOH A 398 SITE 1 AC2 2 TYR A 23 ASN A 113 SITE 1 AC3 3 SER A 24 GLY A 26 GLN A 121 SITE 1 AC4 5 ASN A 65 GLY A 67 ARG A 68 THR A 69 SITE 2 AC4 5 SER A 72 SITE 1 AC5 6 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AC5 6 HOH A 382 HOH A 383 SITE 1 AC6 5 ALA A 11 HIS A 15 CL A 207 CL A 208 SITE 2 AC6 5 HOH A 301 SITE 1 AC7 2 ARG A 14 RU1 A 206 SITE 1 AC8 5 HIS A 15 ASP A 87 ILE A 88 RU1 A 206 SITE 2 AC8 5 HOH A 301 SITE 1 AC9 7 ASP A 18 ASN A 19 ARG A 61 CL A 210 SITE 2 AC9 7 CL A 211 RU1 A 212 CL A 213 SITE 1 AD1 6 ASP A 18 LEU A 25 ILE A 124 RU1 A 209 SITE 2 AD1 6 RU1 A 212 CL A 213 SITE 1 AD2 4 ASP A 18 SER A 24 LEU A 25 RU1 A 209 SITE 1 AD3 6 ASP A 18 PRO A 70 RU1 A 209 CL A 210 SITE 2 AD3 6 CL A 213 HOH A 330 SITE 1 AD4 5 LYS A 13 ASP A 18 RU1 A 209 CL A 210 SITE 2 AD4 5 RU1 A 212 SITE 1 AD5 5 ASP A 52 DMF A 201 HOH A 398 HOH A 399 SITE 2 AD5 5 HOH A 410 SITE 1 AD6 1 ASP A 101 SITE 1 AD7 1 ASP A 101 SITE 1 AD8 2 ASP A 119 CL A 218 SITE 1 AD9 4 ASP A 119 GLN A 121 ALA A 122 RU A 217 SITE 1 AE1 3 LYS A 13 LEU A 129 HOH A 364 SITE 1 AE2 3 LYS A 13 LEU A 129 HOH A 330 CRYST1 79.034 79.034 36.920 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 0.012653 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027086 0.00000