HEADER HYDROLASE 24-JAN-24 8RSI TITLE CRYSTAL STRUCTURE OF METHANOBREVIBACTER ORALIS MACRODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-ACETYL-ADP-RIBOSE DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METHONOBREVIBACTER ORALIS MACRODOMAIN; COMPND 5 EC: 3.5.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOBREVIBACTER ORALIS; SOURCE 3 ORGANISM_TAXID: 66851; SOURCE 4 GENE: YMDB, MBORA_13990; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADP-RIBOSYLATION, ADP-RIBOSE, ADP-RIBOSYLHYDROLASE, LIPOYLATION, KEYWDS 2 METALLOENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ARIZA REVDAT 3 16-OCT-24 8RSI 1 JRNL REVDAT 2 02-OCT-24 8RSI 1 JRNL REVDAT 1 25-SEP-24 8RSI 0 JRNL AUTH A.ARIZA,Q.LIU,N.P.COWIESON,I.AHEL,D.V.FILIPPOV,J.G.M.RACK JRNL TITL EVOLUTIONARY AND MOLECULAR BASIS OF ADP-RIBOSYLATION JRNL TITL 2 REVERSAL BY ZINC-DEPENDENT MACRODOMAINS. JRNL REF J.BIOL.CHEM. V. 300 07770 2024 JRNL REFN ESSN 1083-351X JRNL PMID 39270823 JRNL DOI 10.1016/J.JBC.2024.107770 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0415 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) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 37960 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) : 0.193 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.739 REMARK 3 FREE R VALUE TEST SET COUNT : 1799 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) : 2.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2528 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07600 REMARK 3 B22 (A**2) : 1.58500 REMARK 3 B33 (A**2) : -0.50900 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): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.071 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4559 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4432 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6179 ; 1.729 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10298 ; 0.580 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 607 ; 6.413 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ; 7.770 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 908 ;17.110 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 692 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5387 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1041 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 908 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 89 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2161 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 169 ; 0.181 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.101 ; 0.200 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): 2175 ; 3.008 ; 2.965 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2175 ; 3.007 ; 2.966 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2737 ; 4.373 ; 5.311 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2738 ; 4.372 ; 5.312 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2384 ; 4.227 ; 3.444 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2383 ; 4.167 ; 3.444 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3395 ; 6.243 ; 6.132 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3396 ; 6.243 ; 6.133 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 259 NULL REMARK 3 1 A 0 A 259 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9820 19.9490 -20.4122 REMARK 3 T TENSOR REMARK 3 T11: 0.0089 T22: 0.0783 REMARK 3 T33: 0.1420 T12: -0.0162 REMARK 3 T13: 0.0280 T23: -0.0368 REMARK 3 L TENSOR REMARK 3 L11: 2.8899 L22: 0.7745 REMARK 3 L33: 0.6737 L12: 0.3260 REMARK 3 L13: -0.6425 L23: -0.4936 REMARK 3 S TENSOR REMARK 3 S11: -0.0863 S12: 0.0331 S13: -0.6003 REMARK 3 S21: -0.0164 S22: -0.0723 S23: -0.0820 REMARK 3 S31: 0.0442 S32: 0.0622 S33: 0.1586 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -40.7428 22.4639 -11.9521 REMARK 3 T TENSOR REMARK 3 T11: 0.0153 T22: 0.1811 REMARK 3 T33: 0.0520 T12: -0.0296 REMARK 3 T13: 0.0066 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.6772 L22: 1.6938 REMARK 3 L33: 2.7077 L12: 0.0110 REMARK 3 L13: 0.0177 L23: 0.2550 REMARK 3 S TENSOR REMARK 3 S11: -0.0429 S12: -0.0174 S13: -0.0450 REMARK 3 S21: 0.0553 S22: 0.1556 S23: 0.2250 REMARK 3 S31: 0.1606 S32: -0.3377 S33: -0.1127 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 0.0000 0.0000 0.0000 REMARK 3 T TENSOR REMARK 3 T11: 0.0503 T22: 0.0503 REMARK 3 T33: 0.0503 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 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 8RSI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292136072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28229 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38093 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.059 REMARK 200 RESOLUTION RANGE LOW (A) : 146.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 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 : 0.900 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 (%): 51.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 46.8 MM MES MONOHYDRATE, 53.2 MM REMARK 280 IMIDAZOLE, 20% (V/V) ETHYLENE GLYCOL, 10% (W/V) PEG8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-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 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 35.16000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 73.30450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.16000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 73.30450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 ASN A 260 REMARK 465 GLY B -1 REMARK 465 ASN B 260 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 OD1 ASP A 4 O HOH A 401 2.14 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 OG SER A 75 NH1 ARG B 224 4555 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 183 CD GLU A 183 OE2 0.080 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 B 224 NE - CZ - NH1 ANGL. DEV. = -3.0 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 SER A 45 168.27 174.96 REMARK 500 ASN A 113 50.44 -103.40 REMARK 500 ASN A 113 37.85 -93.97 REMARK 500 TYR A 153 -121.14 55.27 REMARK 500 SER A 207 -9.98 79.10 REMARK 500 SER B 45 164.21 170.70 REMARK 500 ASN B 46 128.07 -36.72 REMARK 500 SER B 92 58.73 -91.47 REMARK 500 MET B 111 -0.09 74.74 REMARK 500 ASN B 113 51.94 -103.24 REMARK 500 ASN B 113 43.41 -96.74 REMARK 500 TYR B 153 -118.09 55.50 REMARK 500 SER B 207 -8.70 78.57 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 224 0.17 SIDE CHAIN 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 107 SG REMARK 620 2 HIS A 112 ND1 116.2 REMARK 620 3 CYS A 114 SG 111.6 105.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 107 SG REMARK 620 2 HIS B 112 ND1 123.0 REMARK 620 3 CYS B 114 SG 114.4 105.7 REMARK 620 4 HOH B 474 O 107.4 99.6 104.3 REMARK 620 N 1 2 3 DBREF1 8RSI A 1 260 UNP A0A166ACJ5_9EURY DBREF2 8RSI A A0A166ACJ5 1 260 DBREF1 8RSI B 1 260 UNP A0A166ACJ5_9EURY DBREF2 8RSI B A0A166ACJ5 1 260 SEQADV 8RSI GLY A -1 UNP A0A166ACJ EXPRESSION TAG SEQADV 8RSI PRO A 0 UNP A0A166ACJ EXPRESSION TAG SEQADV 8RSI GLY B -1 UNP A0A166ACJ EXPRESSION TAG SEQADV 8RSI PRO B 0 UNP A0A166ACJ EXPRESSION TAG SEQRES 1 A 262 GLY PRO MET ASN ASN ASP GLU GLN LEU GLU PHE LEU ILE SEQRES 2 A 262 ASN TYR LEU LEU ASP GLU ARG SER GLU SER ILE ASP ILE SEQRES 3 A 262 PRO LYS THR PHE SER GLU LYS ARG ASN LEU LEU ARG SER SEQRES 4 A 262 LEU MET ASN MET ARG HIS PRO SER ASN ILE SER GLU GLU SEQRES 5 A 262 PHE LEU ARG ILE GLN ASP GLU PHE LEU SER ARG GLU THR SEQRES 6 A 262 ALA ASN LYS ASN LEU THR SER VAL GLU ASP ILE SER LEU SEQRES 7 A 262 SER SER GLY LYS ILE MET LEU TRP GLN GLY ASP ILE THR SEQRES 8 A 262 THR LEU SER ALA ASP ALA ILE VAL ASN ALA ALA ASN SER SEQRES 9 A 262 LYS LEU LEU GLY CYS PHE ILE PRO MET HIS ASN CYS ILE SEQRES 10 A 262 ASP ASN ILE ILE HIS SER ALA SER GLY LEU GLN LEU ARG SEQRES 11 A 262 GLU GLU CYS ASN ARG MET ILE MET LEU GLN GLY GLY ASP SEQRES 12 A 262 GLU ASP VAL GLY LYS ALA LYS ILE THR ASN ALA TYR ASN SEQRES 13 A 262 LEU PRO SER LYS TYR VAL VAL HIS THR VAL GLY PRO SER SEQRES 14 A 262 ILE GLU ARG GLY MET ARG VAL SER SER ASP ASP VAL LYS SEQRES 15 A 262 LYS LEU GLU ARG CYS TYR ASN SER CYS LEU GLU LEU ALA SEQRES 16 A 262 SER GLU TYR LYS LEU ASN SER ILE ALA PHE CYS CYS ILE SEQRES 17 A 262 SER THR GLY VAL PHE ASN PHE PRO GLN LYS LYS ALA ALA SEQRES 18 A 262 GLU ILE ALA ILE ARG THR VAL LYS ASP PHE LEU ASN SER SEQRES 19 A 262 ASN GLU THR SER LEU ASN HIS ILE ILE PHE ASP VAL PHE SEQRES 20 A 262 THR ASP LYS ASP TYR ASP ILE TYR LYS LYS LEU LEU PHE SEQRES 21 A 262 GLY ASN SEQRES 1 B 262 GLY PRO MET ASN ASN ASP GLU GLN LEU GLU PHE LEU ILE SEQRES 2 B 262 ASN TYR LEU LEU ASP GLU ARG SER GLU SER ILE ASP ILE SEQRES 3 B 262 PRO LYS THR PHE SER GLU LYS ARG ASN LEU LEU ARG SER SEQRES 4 B 262 LEU MET ASN MET ARG HIS PRO SER ASN ILE SER GLU GLU SEQRES 5 B 262 PHE LEU ARG ILE GLN ASP GLU PHE LEU SER ARG GLU THR SEQRES 6 B 262 ALA ASN LYS ASN LEU THR SER VAL GLU ASP ILE SER LEU SEQRES 7 B 262 SER SER GLY LYS ILE MET LEU TRP GLN GLY ASP ILE THR SEQRES 8 B 262 THR LEU SER ALA ASP ALA ILE VAL ASN ALA ALA ASN SER SEQRES 9 B 262 LYS LEU LEU GLY CYS PHE ILE PRO MET HIS ASN CYS ILE SEQRES 10 B 262 ASP ASN ILE ILE HIS SER ALA SER GLY LEU GLN LEU ARG SEQRES 11 B 262 GLU GLU CYS ASN ARG MET ILE MET LEU GLN GLY GLY ASP SEQRES 12 B 262 GLU ASP VAL GLY LYS ALA LYS ILE THR ASN ALA TYR ASN SEQRES 13 B 262 LEU PRO SER LYS TYR VAL VAL HIS THR VAL GLY PRO SER SEQRES 14 B 262 ILE GLU ARG GLY MET ARG VAL SER SER ASP ASP VAL LYS SEQRES 15 B 262 LYS LEU GLU ARG CYS TYR ASN SER CYS LEU GLU LEU ALA SEQRES 16 B 262 SER GLU TYR LYS LEU ASN SER ILE ALA PHE CYS CYS ILE SEQRES 17 B 262 SER THR GLY VAL PHE ASN PHE PRO GLN LYS LYS ALA ALA SEQRES 18 B 262 GLU ILE ALA ILE ARG THR VAL LYS ASP PHE LEU ASN SER SEQRES 19 B 262 ASN GLU THR SER LEU ASN HIS ILE ILE PHE ASP VAL PHE SEQRES 20 B 262 THR ASP LYS ASP TYR ASP ILE TYR LYS LYS LEU LEU PHE SEQRES 21 B 262 GLY ASN HET ZN A 301 1 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET ZN B 301 1 HET EDO B 302 4 HET EDO B 303 4 HET EDO B 304 4 HET MES B 305 12 HET GLU B 306 10 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM GLU GLUTAMIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 EDO 9(C2 H6 O2) FORMUL 14 MES C6 H13 N O4 S FORMUL 15 GLU C5 H9 N O4 FORMUL 16 HOH *169(H2 O) HELIX 1 AA1 ASN A 2 ARG A 18 1 17 HELIX 2 AA2 THR A 27 ARG A 42 1 16 HELIX 3 AA3 SER A 48 LYS A 66 1 19 HELIX 4 AA4 SER A 70 ILE A 74 5 5 HELIX 5 AA5 ASP A 87 LEU A 91 5 5 HELIX 6 AA6 CYS A 114 GLY A 124 1 11 HELIX 7 AA7 GLY A 124 GLY A 139 1 16 HELIX 8 AA8 SER A 175 TYR A 196 1 22 HELIX 9 AA9 THR A 208 ASN A 212 5 5 HELIX 10 AB1 PRO A 214 ASN A 233 1 20 HELIX 11 AB2 THR A 246 GLY A 259 1 14 HELIX 12 AB3 ASN B 2 ARG B 18 1 17 HELIX 13 AB4 THR B 27 ARG B 42 1 16 HELIX 14 AB5 SER B 48 LYS B 66 1 19 HELIX 15 AB6 SER B 70 ILE B 74 5 5 HELIX 16 AB7 ASP B 87 LEU B 91 5 5 HELIX 17 AB8 CYS B 114 GLY B 124 1 11 HELIX 18 AB9 GLY B 124 GLY B 139 1 16 HELIX 19 AC1 SER B 175 TYR B 196 1 22 HELIX 20 AC2 THR B 208 ASN B 212 5 5 HELIX 21 AC3 PRO B 214 ASN B 233 1 20 HELIX 22 AC4 THR B 246 GLY B 259 1 14 SHEET 1 AA1 7 SER A 77 SER A 78 0 SHEET 2 AA1 7 ILE A 81 GLN A 85 -1 O ILE A 81 N SER A 78 SHEET 3 AA1 7 HIS A 239 VAL A 244 1 O PHE A 242 N MET A 82 SHEET 4 AA1 7 SER A 200 PHE A 203 1 N ILE A 201 O ILE A 241 SHEET 5 AA1 7 ALA A 95 ALA A 100 1 N VAL A 97 O ALA A 202 SHEET 6 AA1 7 TYR A 159 VAL A 164 1 O VAL A 161 N ASN A 98 SHEET 7 AA1 7 LYS A 148 ASN A 151 -1 N LYS A 148 O HIS A 162 SHEET 1 AA2 7 LEU B 76 SER B 78 0 SHEET 2 AA2 7 ILE B 81 GLN B 85 -1 O ILE B 81 N SER B 78 SHEET 3 AA2 7 HIS B 239 VAL B 244 1 O PHE B 242 N MET B 82 SHEET 4 AA2 7 SER B 200 PHE B 203 1 N PHE B 203 O ASP B 243 SHEET 5 AA2 7 ALA B 95 ALA B 100 1 N VAL B 97 O ALA B 202 SHEET 6 AA2 7 TYR B 159 VAL B 164 1 O VAL B 161 N ILE B 96 SHEET 7 AA2 7 LYS B 148 ASN B 151 -1 N LYS B 148 O HIS B 162 LINK SG CYS A 107 ZN ZN A 301 1555 1555 2.34 LINK ND1 HIS A 112 ZN ZN A 301 1555 1555 2.12 LINK SG CYS A 114 ZN ZN A 301 1555 1555 2.32 LINK SG CYS B 107 ZN ZN B 301 1555 1555 2.29 LINK ND1 HIS B 112 ZN ZN B 301 1555 1555 2.02 LINK SG CYS B 114 ZN ZN B 301 1555 1555 2.41 LINK ZN ZN B 301 O HOH B 474 1555 1555 2.35 CRYST1 70.320 146.609 58.295 90.00 90.00 90.00 P 21 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 0.014221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017154 0.00000