HEADER HYDROLASE 24-AUG-18 6HH5 TITLE ADP-RIBOSYLSERINE HYDROLASE ARH3 OF LATIMERIA CHALUMNAE IN COMPLEX TITLE 2 WITH ADP-HPM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLHYDROLASE LIKE 2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LATIMERIA CHALUMNAE; SOURCE 3 ORGANISM_COMMON: WEST INDIAN OCEAN COELACANTH; SOURCE 4 ORGANISM_TAXID: 7897; SOURCE 5 GENE: ADPRHL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADP-RIBOSYLATION, ADP-RIBOSE, ADPRHL2, ADP-RIBOSYLHYDROLASE LIKE 2, KEYWDS 2 HYDROLASE, ADP-HPM EXPDTA X-RAY DIFFRACTION AUTHOR A.ARIZA REVDAT 4 17-JAN-24 6HH5 1 LINK REVDAT 3 02-JAN-19 6HH5 1 JRNL REVDAT 2 05-DEC-18 6HH5 1 JRNL REVDAT 1 28-NOV-18 6HH5 0 JRNL AUTH J.G.M.RACK,A.ARIZA,B.S.DROWN,C.HENFREY,E.BARTLETT,T.SHIRAI, JRNL AUTH 2 P.J.HERGENROTHER,I.AHEL JRNL TITL (ADP-RIBOSYL)HYDROLASES: STRUCTURAL BASIS FOR DIFFERENTIAL JRNL TITL 2 SUBSTRATE RECOGNITION AND INHIBITION. JRNL REF CELL CHEM BIOL V. 25 1533 2018 JRNL REFN ESSN 2451-9448 JRNL PMID 30472116 JRNL DOI 10.1016/J.CHEMBIOL.2018.11.001 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 48647 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2508 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3720 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5043 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.09000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 1.27000 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): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.151 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.706 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5308 ; 0.011 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 4847 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7175 ; 1.456 ; 1.675 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11379 ; 1.016 ; 1.657 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 698 ;17.468 ; 5.337 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 253 ;32.648 ;23.162 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 907 ;15.242 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;19.370 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 700 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6340 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 950 ; 0.001 ; 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): 2642 ; 1.179 ; 2.180 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2641 ; 1.177 ; 2.180 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3302 ; 1.922 ; 3.265 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3303 ; 1.921 ; 3.266 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2666 ; 1.545 ; 2.315 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2666 ; 1.544 ; 2.315 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3861 ; 2.041 ; 3.407 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6169 ; 6.588 ;26.802 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6125 ; 6.545 ;26.375 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 9 353 B 9 353 10771 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 9 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): -16.1820 -11.6220 10.6820 REMARK 3 T TENSOR REMARK 3 T11: 0.0291 T22: 0.6510 REMARK 3 T33: 0.4040 T12: 0.0448 REMARK 3 T13: 0.0204 T23: -0.0669 REMARK 3 L TENSOR REMARK 3 L11: 4.7585 L22: 3.2037 REMARK 3 L33: 2.0324 L12: -1.0290 REMARK 3 L13: -0.5678 L23: 0.0757 REMARK 3 S TENSOR REMARK 3 S11: 0.2197 S12: 0.9234 S13: 0.3612 REMARK 3 S21: -0.2768 S22: -0.0574 S23: -0.1219 REMARK 3 S31: -0.0628 S32: -0.0392 S33: -0.1624 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 9 B 601 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1410 11.3320 10.0150 REMARK 3 T TENSOR REMARK 3 T11: 0.0156 T22: 0.3302 REMARK 3 T33: 0.3473 T12: 0.0063 REMARK 3 T13: 0.0221 T23: 0.1272 REMARK 3 L TENSOR REMARK 3 L11: 2.4171 L22: 2.9420 REMARK 3 L33: 1.6956 L12: -0.3736 REMARK 3 L13: 0.1359 L23: 0.0125 REMARK 3 S TENSOR REMARK 3 S11: -0.0096 S12: 0.0209 S13: -0.1776 REMARK 3 S21: -0.2006 S22: -0.0083 S23: 0.0056 REMARK 3 S31: -0.0181 S32: 0.0465 S33: 0.0179 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 6HH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011662. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 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 : XDS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 44.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 1.83700 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: 2FOZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM ACETATE, 25 % (W/V), REMARK 280 PEG4000, 100 MM CITRATE PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 33.43450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.77700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.08900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.77700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.43450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.08900 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 7 REMARK 465 PRO A 8 REMARK 465 GLY A 211 REMARK 465 GLU A 212 REMARK 465 MET A 213 REMARK 465 SER A 214 REMARK 465 ALA A 215 REMARK 465 SER A 216 REMARK 465 ASP A 217 REMARK 465 ALA A 218 REMARK 465 GLY A 219 REMARK 465 GLU A 220 REMARK 465 HIS A 221 REMARK 465 ASP A 222 REMARK 465 ARG A 223 REMARK 465 PRO A 224 REMARK 465 ASN A 225 REMARK 465 GLU A 226 REMARK 465 VAL A 227 REMARK 465 LYS A 228 REMARK 465 LYS A 354 REMARK 465 THR A 355 REMARK 465 PRO A 356 REMARK 465 GLY B 7 REMARK 465 PRO B 8 REMARK 465 GLY B 211 REMARK 465 GLU B 212 REMARK 465 MET B 213 REMARK 465 SER B 214 REMARK 465 ALA B 215 REMARK 465 SER B 216 REMARK 465 ASP B 217 REMARK 465 ALA B 218 REMARK 465 GLY B 219 REMARK 465 GLU B 220 REMARK 465 HIS B 221 REMARK 465 ASP B 222 REMARK 465 ARG B 223 REMARK 465 PRO B 224 REMARK 465 ASN B 225 REMARK 465 GLU B 226 REMARK 465 VAL B 227 REMARK 465 LYS B 354 REMARK 465 THR B 355 REMARK 465 PRO B 356 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 B 26 OD1 ASP B 305 2.11 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 THR A 62 -160.19 -118.97 REMARK 500 PHE A 81 107.71 81.85 REMARK 500 GLU A 191 76.90 -64.57 REMARK 500 HIS A 258 43.76 -143.68 REMARK 500 SER A 265 -41.48 -137.88 REMARK 500 THR B 62 -162.00 -120.32 REMARK 500 PHE B 81 106.93 83.31 REMARK 500 GLN B 189 57.65 -92.55 REMARK 500 GLU B 191 74.60 -57.68 REMARK 500 LEU B 229 78.12 -109.86 REMARK 500 HIS B 258 44.37 -146.17 REMARK 500 SER B 265 -40.81 -136.70 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 16 0.26 SIDE CHAIN REMARK 500 ARG A 126 0.07 SIDE CHAIN REMARK 500 ARG A 234 0.17 SIDE CHAIN REMARK 500 ARG B 89 0.10 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 62 OG1 REMARK 620 2 ASP A 63 OD1 85.3 REMARK 620 3 ASP A 64 OD1 88.9 82.0 REMARK 620 4 ASP A 305 OD2 87.6 156.9 119.9 REMARK 620 5 ASP A 305 OD2 90.5 153.5 124.2 5.1 REMARK 620 6 HOH A 518 O 154.0 118.0 83.6 74.9 73.6 REMARK 620 7 HOH A 540 O 97.8 76.6 156.9 82.6 78.1 98.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 62 OG1 REMARK 620 2 ASP B 63 OD1 84.6 REMARK 620 3 ASP B 64 OD1 84.6 83.2 REMARK 620 4 ASP B 305 OD2 88.4 160.6 114.2 REMARK 620 5 ASP B 305 OD2 72.7 154.8 104.9 17.2 REMARK 620 6 HOH B 535 O 153.4 119.0 86.3 72.7 85.6 REMARK 620 7 HOH B 604 O 97.5 81.9 164.7 81.0 90.1 97.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A3R A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A3R B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 DBREF 6HH5 A 10 356 UNP H3BCW1 H3BCW1_LATCH 10 356 DBREF 6HH5 B 10 356 UNP H3BCW1 H3BCW1_LATCH 10 356 SEQADV 6HH5 GLY A 7 UNP H3BCW1 EXPRESSION TAG SEQADV 6HH5 PRO A 8 UNP H3BCW1 EXPRESSION TAG SEQADV 6HH5 MET A 9 UNP H3BCW1 EXPRESSION TAG SEQADV 6HH5 GLY B 7 UNP H3BCW1 EXPRESSION TAG SEQADV 6HH5 PRO B 8 UNP H3BCW1 EXPRESSION TAG SEQADV 6HH5 MET B 9 UNP H3BCW1 EXPRESSION TAG SEQRES 1 A 350 GLY PRO MET VAL SER LEU ALA GLN VAL ARG GLY ALA LEU SEQRES 2 A 350 CYS GLY ALA LEU LEU GLY ASP CYS MET GLY ALA GLU PHE SEQRES 3 A 350 GLU GLY SER ASP ALA VAL GLU LEU PRO ASP VAL LEU GLU SEQRES 4 A 350 PHE VAL ARG LEU LEU GLU LYS GLU LYS LYS ALA GLY THR SEQRES 5 A 350 LEU PHE TYR THR ASP ASP THR ALA MET THR ARG ALA VAL SEQRES 6 A 350 ILE GLN SER LEU ILE ALA LYS PRO ASP PHE ASP GLU VAL SEQRES 7 A 350 ASP MET ALA LYS ARG PHE ALA GLU GLU TYR LYS LYS GLU SEQRES 8 A 350 PRO THR ARG GLY TYR GLY ALA GLY VAL VAL GLN VAL PHE SEQRES 9 A 350 LYS LYS LEU LEU SER PRO LYS TYR SER ASP VAL PHE GLN SEQRES 10 A 350 PRO ALA ARG GLU GLN PHE ASP GLY LYS GLY SER TYR GLY SEQRES 11 A 350 ASN GLY GLY ALA MET ARG VAL ALA SER ILE ALA LEU ALA SEQRES 12 A 350 TYR PRO ASN ILE GLN ASP VAL ILE LYS PHE ALA ARG ARG SEQRES 13 A 350 SER ALA GLN LEU THR HIS ALA SER PRO LEU GLY TYR ASN SEQRES 14 A 350 GLY ALA ILE LEU GLN ALA LEU ALA VAL HIS PHE ALA LEU SEQRES 15 A 350 GLN GLY GLU LEU LYS ARG ASP THR PHE LEU GLU GLN LEU SEQRES 16 A 350 ILE GLY GLU MET GLU ARG ILE GLU GLY GLY GLU MET SER SEQRES 17 A 350 ALA SER ASP ALA GLY GLU HIS ASP ARG PRO ASN GLU VAL SEQRES 18 A 350 LYS LEU PRO PHE CYS SER ARG LEU LYS LYS ILE LYS GLU SEQRES 19 A 350 PHE LEU ALA SER SER ASN VAL PRO LYS ALA ASP ILE VAL SEQRES 20 A 350 ASP GLU LEU GLY HIS GLY ILE ALA ALA LEU GLU SER VAL SEQRES 21 A 350 PRO THR ALA ILE TYR SER PHE LEU HIS CYS MET GLU SER SEQRES 22 A 350 ASP PRO ASP ILE PRO ASP LEU TYR ASN ASN LEU GLN ARG SEQRES 23 A 350 THR ILE ILE TYR SER ILE SER LEU GLY GLY ASP THR ASP SEQRES 24 A 350 THR ILE ALA THR MET ALA GLY ALA ILE ALA GLY ALA TYR SEQRES 25 A 350 TYR GLY MET ASP GLN VAL THR PRO SER TRP LYS ARG SER SEQRES 26 A 350 CYS GLU ALA ILE VAL GLU THR GLU GLU SER ALA VAL LYS SEQRES 27 A 350 LEU TYR GLU LEU TYR CYS LYS GLN LEU LYS THR PRO SEQRES 1 B 350 GLY PRO MET VAL SER LEU ALA GLN VAL ARG GLY ALA LEU SEQRES 2 B 350 CYS GLY ALA LEU LEU GLY ASP CYS MET GLY ALA GLU PHE SEQRES 3 B 350 GLU GLY SER ASP ALA VAL GLU LEU PRO ASP VAL LEU GLU SEQRES 4 B 350 PHE VAL ARG LEU LEU GLU LYS GLU LYS LYS ALA GLY THR SEQRES 5 B 350 LEU PHE TYR THR ASP ASP THR ALA MET THR ARG ALA VAL SEQRES 6 B 350 ILE GLN SER LEU ILE ALA LYS PRO ASP PHE ASP GLU VAL SEQRES 7 B 350 ASP MET ALA LYS ARG PHE ALA GLU GLU TYR LYS LYS GLU SEQRES 8 B 350 PRO THR ARG GLY TYR GLY ALA GLY VAL VAL GLN VAL PHE SEQRES 9 B 350 LYS LYS LEU LEU SER PRO LYS TYR SER ASP VAL PHE GLN SEQRES 10 B 350 PRO ALA ARG GLU GLN PHE ASP GLY LYS GLY SER TYR GLY SEQRES 11 B 350 ASN GLY GLY ALA MET ARG VAL ALA SER ILE ALA LEU ALA SEQRES 12 B 350 TYR PRO ASN ILE GLN ASP VAL ILE LYS PHE ALA ARG ARG SEQRES 13 B 350 SER ALA GLN LEU THR HIS ALA SER PRO LEU GLY TYR ASN SEQRES 14 B 350 GLY ALA ILE LEU GLN ALA LEU ALA VAL HIS PHE ALA LEU SEQRES 15 B 350 GLN GLY GLU LEU LYS ARG ASP THR PHE LEU GLU GLN LEU SEQRES 16 B 350 ILE GLY GLU MET GLU ARG ILE GLU GLY GLY GLU MET SER SEQRES 17 B 350 ALA SER ASP ALA GLY GLU HIS ASP ARG PRO ASN GLU VAL SEQRES 18 B 350 LYS LEU PRO PHE CYS SER ARG LEU LYS LYS ILE LYS GLU SEQRES 19 B 350 PHE LEU ALA SER SER ASN VAL PRO LYS ALA ASP ILE VAL SEQRES 20 B 350 ASP GLU LEU GLY HIS GLY ILE ALA ALA LEU GLU SER VAL SEQRES 21 B 350 PRO THR ALA ILE TYR SER PHE LEU HIS CYS MET GLU SER SEQRES 22 B 350 ASP PRO ASP ILE PRO ASP LEU TYR ASN ASN LEU GLN ARG SEQRES 23 B 350 THR ILE ILE TYR SER ILE SER LEU GLY GLY ASP THR ASP SEQRES 24 B 350 THR ILE ALA THR MET ALA GLY ALA ILE ALA GLY ALA TYR SEQRES 25 B 350 TYR GLY MET ASP GLN VAL THR PRO SER TRP LYS ARG SER SEQRES 26 B 350 CYS GLU ALA ILE VAL GLU THR GLU GLU SER ALA VAL LYS SEQRES 27 B 350 LEU TYR GLU LEU TYR CYS LYS GLN LEU LYS THR PRO HET MG A 401 1 HET A3R A 402 34 HET GOL A 403 6 HET MG B 401 1 HET A3R B 402 34 HET GOL B 403 6 HETNAM MG MAGNESIUM ION HETNAM A3R ADENOSINE DIPHOSPHATE (HYDROXYMETHYL)PYRROLIDINE HETNAM 2 A3R MONOALCOHOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 2(MG 2+) FORMUL 4 A3R 2(C15 H24 N6 O11 P2) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 9 HOH *255(H2 O) HELIX 1 AA1 SER A 11 ALA A 30 1 20 HELIX 2 AA2 GLU A 31 GLU A 33 5 3 HELIX 3 AA3 GLU A 39 GLU A 51 1 13 HELIX 4 AA4 THR A 62 LYS A 78 1 17 HELIX 5 AA5 ASP A 82 GLU A 97 1 16 HELIX 6 AA6 GLY A 105 SER A 115 1 11 HELIX 7 AA7 PHE A 122 LYS A 132 1 11 HELIX 8 AA8 ASN A 137 ARG A 142 1 6 HELIX 9 AA9 VAL A 143 TYR A 150 1 8 HELIX 10 AB1 ASN A 152 LEU A 166 1 15 HELIX 11 AB2 SER A 170 LEU A 188 1 19 HELIX 12 AB3 LYS A 193 GLY A 210 1 18 HELIX 13 AB4 PRO A 230 SER A 244 1 15 HELIX 14 AB5 PRO A 248 GLY A 257 1 10 HELIX 15 AB6 ALA A 261 GLU A 264 5 4 HELIX 16 AB7 SER A 265 CYS A 276 1 12 HELIX 17 AB8 ASN A 288 LEU A 300 1 13 HELIX 18 AB9 ASP A 303 GLY A 320 1 18 HELIX 19 AC1 MET A 321 VAL A 324 5 4 HELIX 20 AC2 THR A 325 ARG A 330 1 6 HELIX 21 AC3 ALA A 334 LEU A 353 1 20 HELIX 22 AC4 SER B 11 GLU B 31 1 21 HELIX 23 AC5 GLU B 39 GLU B 51 1 13 HELIX 24 AC6 THR B 62 LYS B 78 1 17 HELIX 25 AC7 ASP B 82 GLU B 97 1 16 HELIX 26 AC8 GLY B 105 SER B 115 1 11 HELIX 27 AC9 PHE B 122 LYS B 132 1 11 HELIX 28 AD1 ASN B 137 ARG B 142 1 6 HELIX 29 AD2 VAL B 143 TYR B 150 1 8 HELIX 30 AD3 ASN B 152 LEU B 166 1 15 HELIX 31 AD4 SER B 170 GLN B 189 1 20 HELIX 32 AD5 LYS B 193 GLY B 210 1 18 HELIX 33 AD6 LEU B 229 SER B 244 1 16 HELIX 34 AD7 PRO B 248 GLY B 257 1 10 HELIX 35 AD8 ALA B 261 GLU B 264 5 4 HELIX 36 AD9 SER B 265 CYS B 276 1 12 HELIX 37 AE1 ASN B 288 LEU B 300 1 13 HELIX 38 AE2 ASP B 303 GLY B 320 1 18 HELIX 39 AE3 MET B 321 VAL B 324 5 4 HELIX 40 AE4 THR B 325 ARG B 330 1 6 HELIX 41 AE5 ALA B 334 LEU B 353 1 20 LINK OG1 THR A 62 MG MG A 401 1555 1555 2.20 LINK OD1 ASP A 63 MG MG A 401 1555 1555 2.26 LINK OD1 ASP A 64 MG MG A 401 1555 1555 2.21 LINK OD2AASP A 305 MG MG A 401 1555 1555 2.22 LINK OD2BASP A 305 MG MG A 401 1555 1555 2.24 LINK MG MG A 401 O HOH A 518 1555 1555 2.18 LINK MG MG A 401 O HOH A 540 1555 1555 2.21 LINK OG1 THR B 62 MG MG B 401 1555 1555 2.20 LINK OD1 ASP B 63 MG MG B 401 1555 1555 2.26 LINK OD1 ASP B 64 MG MG B 401 1555 1555 2.24 LINK OD2AASP B 305 MG MG B 401 1555 1555 2.26 LINK OD2BASP B 305 MG MG B 401 1555 1555 2.24 LINK MG MG B 401 O HOH B 535 1555 1555 2.19 LINK MG MG B 401 O HOH B 604 1555 1555 2.23 SITE 1 AC1 6 THR A 62 ASP A 63 ASP A 64 ASP A 305 SITE 2 AC1 6 HOH A 518 HOH A 540 SITE 1 AC2 24 GLU A 33 ASP A 63 GLY A 101 GLY A 103 SITE 2 AC2 24 ALA A 104 GLY A 105 VAL A 106 PHE A 129 SITE 3 AC2 24 GLY A 133 SER A 134 TYR A 135 GLY A 136 SITE 4 AC2 24 ASN A 137 GLY A 138 HIS A 168 ILE A 260 SITE 5 AC2 24 ASP A 303 THR A 306 HOH A 518 HOH A 519 SITE 6 AC2 24 HOH A 533 HOH A 539 HOH A 548 ASP B 42 SITE 1 AC3 7 ASP A 80 ASP A 155 PHE A 159 GLN A 352 SITE 2 AC3 7 HOH A 511 SER B 119 HOH B 575 SITE 1 AC4 6 THR B 62 ASP B 63 ASP B 64 ASP B 305 SITE 2 AC4 6 HOH B 535 HOH B 604 SITE 1 AC5 20 ALA A 37 ASP B 63 GLY B 101 GLY B 103 SITE 2 AC5 20 ALA B 104 GLY B 105 VAL B 106 PHE B 129 SITE 3 AC5 20 GLY B 133 SER B 134 TYR B 135 GLY B 136 SITE 4 AC5 20 ASN B 137 GLY B 138 HIS B 168 ILE B 260 SITE 5 AC5 20 HOH B 503 HOH B 528 HOH B 538 HOH B 589 SITE 1 AC6 5 SER B 245 ASN B 246 HIS B 275 PRO B 281 SITE 2 AC6 5 HOH B 515 CRYST1 66.869 98.178 105.554 90.00 90.00 90.00 P 21 21 21 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 0.014955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009474 0.00000