HEADER PROTEIN BINDING 19-JUN-23 8PH6 TITLE X-RAY STRUCTURE OF THE ADDUCT FORMED UPON REACTION OF LYSOZYME WITH TITLE 2 K2[RU2(DPHF)(CO3)3] IN CONDITION B 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 RUTHENIUM, PROTEIN INTERACTION, METALLODRUG, DIRUTHENIUM, HYDROLASE, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.TERAN,G.FERRARO,A.MERLINO REVDAT 2 20-SEP-23 8PH6 1 JRNL REVDAT 1 13-SEP-23 8PH6 0 JRNL AUTH A.TERAN,G.FERRARO,P.IMBIMBO,A.E.SANCHEZ-PELAEZ,D.M.MONTI, JRNL AUTH 2 S.HERRERO,A.MERLINO JRNL TITL STERIC HINDRANCE AND CHARGE INFLUENCE ON THE CYTOTOXIC JRNL TITL 2 ACTIVITY AND PROTEIN BINDING PROPERTIES OF DIRUTHENIUM JRNL TITL 3 COMPLEXES. JRNL REF INT.J.BIOL.MACROMOL. V. 253 26666 2023 JRNL REFN ISSN 0141-8130 JRNL PMID 37660867 JRNL DOI 10.1016/J.IJBIOMAC.2023.126666 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0403 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 49863 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 : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2503 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2848 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 130 REMARK 3 BIN FREE R VALUE : 0.3270 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 : 116 REMARK 3 SOLVENT ATOMS : 196 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.00900 REMARK 3 B22 (A**2) : -0.00900 REMARK 3 B33 (A**2) : 0.01700 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): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.510 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1316 ; 0.012 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 1099 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1829 ; 2.165 ; 1.784 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2521 ; 0.737 ; 1.585 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 157 ; 6.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 9.907 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 197 ;15.100 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 166 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1634 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 338 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 289 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 107 ; 0.264 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 565 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 126 ; 0.268 ; 0.200 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): 592 ; 1.263 ; 1.154 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 592 ; 1.240 ; 1.152 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 761 ; 1.888 ; 2.085 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 762 ; 1.906 ; 2.088 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 724 ; 2.023 ; 1.381 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 603 ; 2.124 ; 1.414 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1068 ; 3.072 ; 2.468 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 880 ; 3.286 ; 2.492 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8PH6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-22 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 54.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.75400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 38.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M SODIUM FORMATE AND 0.1 M HEPES REMARK 280 BUFFER AT PH 7.5, 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 19.30500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.44000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.95750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.44000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.44000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.65250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.44000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.44000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.95750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.44000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.44000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.65250 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 19.30500 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 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 349 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 358 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 361 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 496 LIES ON A SPECIAL POSITION. 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 LEU A 129 O LEU A 129 7554 1.47 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 18 CB - CG - OD2 ANGL. DEV. = -6.0 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 31.05 -96.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 125 0.12 SIDE CHAIN REMARK 500 ARG A 128 0.10 SIDE CHAIN 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 496 DISTANCE = 6.00 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 ZWL A 202 RU1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 ZWL A 202 RU2 89.2 REMARK 620 3 ZWL A 202 O3 88.1 88.8 REMARK 620 4 ZWL A 202 N1 94.3 88.6 176.5 REMARK 620 5 ZWL A 202 O1 176.4 90.6 88.4 89.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZWL A 202 RU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD2 REMARK 620 2 ZWL A 202 O4 89.8 REMARK 620 3 ZWL A 202 N2 92.5 175.5 REMARK 620 4 ZWL A 202 RU1 89.7 90.9 93.0 REMARK 620 5 ZWL A 202 O2 173.1 83.3 94.4 90.6 REMARK 620 6 HOH A 354 O 91.4 76.6 99.5 167.5 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YWV A 203 RU1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 OD1 REMARK 620 2 YWV A 203 RU2 86.0 REMARK 620 3 YWV A 203 N1 176.0 90.2 REMARK 620 4 YWV A 203 O1 93.5 90.0 87.4 REMARK 620 5 ARG A 125 NH2 88.9 87.5 90.0 176.4 REMARK 620 6 ZXE A 205 O8 73.4 159.3 110.5 89.3 94.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YWV A 203 RU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 OD2 REMARK 620 2 YWV A 203 N2 179.3 REMARK 620 3 YWV A 203 O2 91.6 88.9 REMARK 620 4 YWV A 203 RU1 91.1 89.4 89.1 REMARK 620 5 ARG A 125 NH1 84.3 95.3 175.8 91.5 REMARK 620 6 HOH A 429 O 84.5 94.9 95.1 174.0 83.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZWO A 204 RU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 348 O REMARK 620 2 ZWO A 204 N2 99.9 REMARK 620 3 ZWO A 204 O6 91.8 90.9 REMARK 620 4 ZWO A 204 O2 86.9 92.4 176.6 REMARK 620 5 ZWO A 204 RU1 170.7 89.4 88.6 92.2 REMARK 620 6 ZWO A 204 O4 80.1 179.1 88.2 88.5 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZXE A 205 RU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 301 O REMARK 620 2 ZXE A 205 O2 92.9 REMARK 620 3 ZXE A 205 N2 94.7 90.8 REMARK 620 4 ZXE A 205 RU1 173.8 89.6 91.0 REMARK 620 5 ZXE A 205 O4 85.0 91.2 178.0 89.3 REMARK 620 6 ZXE A 205 O6 88.6 178.4 89.6 88.9 88.5 REMARK 620 N 1 2 3 4 5 DBREF 8PH6 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 EPE A 201 15 HET ZWL A 202 26 HET YWV A 203 20 HET ZWO A 204 29 HET ZXE A 205 28 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM ZWL [RU2(DPHF)(FORMATE)(CO3)] HETNAM YWV [RU2(DPHF)(FORMATE)] HETNAM ZWO RU2(DPHF)(CO3)3 HETNAM ZXE RU2(DPHF)(CO3)2(FORMATE) HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 ZWL C15 H14 N2 O5 RU2 FORMUL 4 YWV C14 H14 N2 O2 RU2 FORMUL 5 ZWO C16 H12 N2 O9 RU2 FORMUL 6 ZXE C16 H14 N2 O8 RU2 FORMUL 7 HOH *196(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 2.03 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.05 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 OD1 ASP A 101 RU1 AZWL A 202 1555 1555 1.98 LINK OD2 ASP A 101 RU2 AZWL A 202 1555 1555 2.10 LINK OD1 ASP A 119 RU1 AYWV A 203 1555 1555 2.02 LINK OD2 ASP A 119 RU2 AYWV A 203 1555 1555 2.19 LINK NH1AARG A 125 RU2 AYWV A 203 1555 1555 2.25 LINK NH2AARG A 125 RU1 AYWV A 203 1555 1555 1.94 LINK RU2 AZWL A 202 O AHOH A 354 1555 1555 2.35 LINK RU1 AYWV A 203 O8 ZXE A 205 1555 4445 2.21 LINK RU2 AYWV A 203 O HOH A 429 1555 1555 2.30 LINK RU2 AZWO A 204 O HOH A 348 1555 1555 2.17 LINK RU2 ZXE A 205 O HOH A 301 1555 1555 2.18 CRYST1 76.880 76.880 38.610 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 0.013007 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025900 0.00000