HEADER HYDROLASE 18-JUN-17 5W6X TITLE CRYSTAL STRUCTURE OF THE HSNUDT16 IN COMPLEX WITH MG+2 AND ADP-RIBOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: U8 SNORNA-DECAPPING ENZYME; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDP PHOSPHATASE,IDPASE,INOSINE DIPHOSPHATE PHOSPHATASE, COMPND 5 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 16,NUDIX MOTIF 16,NUDIX COMPND 6 HYDROLASE 16,U8 SNORNA-BINDING PROTEIN H29K,M7GPPPN-MRNA HYDROLASE; COMPND 7 EC: 3.6.1.62,3.6.1.64; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS NUDIX, NUDIX HYDROLASE, DECAPPING ENZYME, DEMODIFICATION OF KEYWDS 2 PARYLATION, MARYLATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.THIRAWATANANOND,S.B.GABELLI REVDAT 4 03-APR-24 5W6X 1 REMARK REVDAT 3 13-MAR-24 5W6X 1 REMARK LINK REVDAT 2 05-JUN-19 5W6X 1 JRNL REVDAT 1 19-DEC-18 5W6X 0 JRNL AUTH P.THIRAWATANANOND,R.L.MCPHERSON,J.MALHI,S.NATHAN, JRNL AUTH 2 M.J.LAMBRECHT,M.BRICHACEK,P.J.HERGENROTHER,A.K.L.LEUNG, JRNL AUTH 3 S.B.GABELLI JRNL TITL STRUCTURAL ANALYSES OF NUDT16-ADP-RIBOSE COMPLEXES DIRECT JRNL TITL 2 RATIONAL DESIGN OF MUTANTS WITH IMPROVED PROCESSING OF JRNL TITL 3 POLY(ADP-RIBOSYL)ATED PROTEINS. JRNL REF SCI REP V. 9 5940 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30976021 JRNL DOI 10.1038/S41598-019-39491-W REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 19245 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 961 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2751 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.01000 REMARK 3 B22 (A**2) : 0.76000 REMARK 3 B33 (A**2) : 0.44000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.272 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 5W6X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20264 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21400 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: AMORE REMARK 200 STARTING MODEL: PDBID XX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CHES, PH 9.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 56.87750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.15950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.87750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.15950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 182 REMARK 465 SER A 183 REMARK 465 GLY A 184 REMARK 465 SER A 185 REMARK 465 ILE A 186 REMARK 465 SER A 187 REMARK 465 GLY A 188 REMARK 465 LEU A 189 REMARK 465 LYS A 190 REMARK 465 ILE A 191 REMARK 465 PRO A 192 REMARK 465 ALA A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 3 REMARK 465 THR B 64 REMARK 465 GLY B 101 REMARK 465 SER B 102 REMARK 465 GLY B 103 REMARK 465 GLN B 182 REMARK 465 SER B 183 REMARK 465 GLY B 184 REMARK 465 SER B 185 REMARK 465 ILE B 186 REMARK 465 SER B 187 REMARK 465 GLY B 188 REMARK 465 LEU B 189 REMARK 465 LYS B 190 REMARK 465 ILE B 191 REMARK 465 PRO B 192 REMARK 465 ALA B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 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 NH2 ARG B 129 O HOH B 501 1.69 REMARK 500 NH2 ARG B 78 OE2 GLU B 83 1.81 REMARK 500 NH1 ARG B 129 O HOH B 502 2.01 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 NH1 ARG B 5 OE1 GLU B 11 2555 2.04 REMARK 500 NH1 ARG B 5 OE2 GLU B 11 2555 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 ARG B 96 N - CA - C ANGL. DEV. = 18.0 DEGREES REMARK 500 ARG B 96 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 42 -62.95 70.93 REMARK 500 LEU A 135 -95.63 -127.27 REMARK 500 VAL A 152 -40.61 -131.96 REMARK 500 LEU A 178 -138.35 -65.02 REMARK 500 LEU A 180 40.81 -81.70 REMARK 500 ARG B 38 -35.03 -137.02 REMARK 500 ARG B 42 -66.99 71.10 REMARK 500 LEU B 135 -90.89 -131.48 REMARK 500 LEU B 135 -92.59 -131.48 REMARK 500 VAL B 152 -50.80 -133.40 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 59 O REMARK 620 2 GLU A 80 OE2 75.6 REMARK 620 3 APR A 401 O1A 101.9 168.9 REMARK 620 4 APR A 401 O1B 91.5 82.3 87.1 REMARK 620 5 HOH A 605 O 92.3 99.6 91.2 176.0 REMARK 620 6 HOH A 613 O 164.6 91.6 89.1 78.1 98.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 76 OE1 REMARK 620 2 GLU A 80 OE2 108.5 REMARK 620 3 GLU A 136 OE2 166.1 85.0 REMARK 620 4 APR A 401 O1B 95.6 82.5 82.3 REMARK 620 5 HOH A 549 O 91.7 159.0 74.6 89.8 REMARK 620 6 HOH A 562 O 84.5 108.2 94.9 168.7 78.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 59 O REMARK 620 2 GLU B 80 OE2 60.0 REMARK 620 3 APR B 401 O1A 89.9 136.1 REMARK 620 4 HOH B 587 O 135.5 92.7 88.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 80 OE2 REMARK 620 2 GLU B 136 OE1 118.4 REMARK 620 3 APR B 401 O2B 94.1 79.2 REMARK 620 4 HOH B 553 O 178.8 61.9 84.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue APR A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue APR B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VY2 RELATED DB: PDB REMARK 900 F36S MUTANT OF THE SAME ENZYME; THIS IS A SUBSTRATE COMPLEX REMARK 900 RELATED ID: 5W6Z RELATED DB: PDB REMARK 900 RELATED ID: 5WJI RELATED DB: PDB REMARK 900 RELATED ID: 6B09 RELATED DB: PDB DBREF 5W6X A 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 DBREF 5W6X B 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 SEQADV 5W6X VAL A 22 UNP Q96DE0 ALA 22 ENGINEERED MUTATION SEQADV 5W6X VAL B 22 UNP Q96DE0 ALA 22 ENGINEERED MUTATION SEQRES 1 A 195 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 A 195 ALA LEU GLY SER GLY TRP ARG HIS VAL CYS HIS ALA LEU SEQRES 3 A 195 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 A 195 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 A 195 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 A 195 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 A 195 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 A 195 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 A 195 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 A 195 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 A 195 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 A 195 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 A 195 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 A 195 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 A 195 SER GLY SER ILE SER GLY LEU LYS ILE PRO ALA HIS HIS SEQRES 1 B 195 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 B 195 ALA LEU GLY SER GLY TRP ARG HIS VAL CYS HIS ALA LEU SEQRES 3 B 195 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 B 195 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 B 195 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 B 195 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 B 195 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 B 195 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 B 195 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 B 195 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 B 195 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 B 195 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 B 195 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 B 195 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 B 195 SER GLY SER ILE SER GLY LEU LYS ILE PRO ALA HIS HIS HET APR A 401 36 HET MG A 402 1 HET MG A 403 1 HET ACY A 404 4 HET APR B 401 36 HET MG B 402 1 HET MG B 403 1 HET ACY B 404 4 HET PEG B 405 7 HETNAM APR ADENOSINE-5-DIPHOSPHORIBOSE HETNAM MG MAGNESIUM ION HETNAM ACY ACETIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 APR 2(C15 H23 N5 O14 P2) FORMUL 4 MG 4(MG 2+) FORMUL 6 ACY 2(C2 H4 O2) FORMUL 11 PEG C4 H10 O3 FORMUL 12 HOH *266(H2 O) HELIX 1 AA1 GLU A 8 ALA A 14 1 7 HELIX 2 AA2 PHE A 36 ARG A 38 5 3 HELIX 3 AA3 SER A 68 GLY A 82 1 15 HELIX 4 AA4 GLU A 83 PHE A 88 5 6 HELIX 5 AA5 GLU A 91 THR A 93 5 3 HELIX 6 AA6 THR A 116 ALA A 127 1 12 HELIX 7 AA7 THR A 128 ALA A 130 5 3 HELIX 8 AA8 GLY A 154 LEU A 159 1 6 HELIX 9 AA9 SER A 166 LEU A 178 1 13 HELIX 10 AB1 GLU B 8 ALA B 14 1 7 HELIX 11 AB2 PHE B 36 ARG B 38 5 3 HELIX 12 AB3 SER B 68 GLY B 82 1 15 HELIX 13 AB4 GLU B 83 PHE B 88 5 6 HELIX 14 AB5 GLU B 91 THR B 93 5 3 HELIX 15 AB6 THR B 116 ALA B 127 1 12 HELIX 16 AB7 THR B 128 ALA B 130 5 3 HELIX 17 AB8 GLY B 154 LEU B 159 1 6 HELIX 18 AB9 SER B 166 LEU B 178 1 13 SHEET 1 AA1 6 ARG A 6 LEU A 7 0 SHEET 2 AA1 6 TYR A 95 VAL A 100 -1 O SER A 98 N LEU A 7 SHEET 3 AA1 6 VAL A 106 ARG A 114 -1 O PHE A 110 N ARG A 96 SHEET 4 AA1 6 ARG A 20 LEU A 35 1 N VAL A 22 O HIS A 109 SHEET 5 AA1 6 ILE A 39 ARG A 50 -1 O ILE A 39 N LEU A 35 SHEET 6 AA1 6 GLY A 59 VAL A 62 0 SHEET 1 AA2 4 LEU A 55 GLY A 56 0 SHEET 2 AA2 4 ILE A 39 ARG A 50 -1 N GLN A 48 O GLY A 56 SHEET 3 AA2 4 ARG A 20 LEU A 35 -1 N LEU A 35 O ILE A 39 SHEET 4 AA2 4 VAL A 137 ARG A 142 0 SHEET 1 AA3 6 ARG B 5 LEU B 7 0 SHEET 2 AA3 6 TYR B 95 VAL B 100 -1 O VAL B 100 N ARG B 5 SHEET 3 AA3 6 VAL B 106 ARG B 114 -1 O ALA B 108 N HIS B 99 SHEET 4 AA3 6 ARG B 20 LEU B 35 1 N VAL B 22 O HIS B 109 SHEET 5 AA3 6 ILE B 39 ARG B 50 -1 O ALA B 44 N ALA B 29 SHEET 6 AA3 6 GLY B 59 PHE B 61 0 SHEET 1 AA4 4 LEU B 55 GLY B 56 0 SHEET 2 AA4 4 ILE B 39 ARG B 50 -1 N GLN B 48 O GLY B 56 SHEET 3 AA4 4 ARG B 20 LEU B 35 -1 N ALA B 29 O ALA B 44 SHEET 4 AA4 4 VAL B 137 ARG B 142 0 LINK O GLY A 59 MG MG A 403 1555 1555 2.35 LINK OE1 GLU A 76 MG MG A 402 1555 1555 2.30 LINK OE2 GLU A 80 MG MG A 402 1555 1555 2.39 LINK OE2 GLU A 80 MG MG A 403 1555 1555 2.32 LINK OE2 GLU A 136 MG MG A 402 1555 1555 2.26 LINK O1B APR A 401 MG MG A 402 1555 1555 2.34 LINK O1A APR A 401 MG MG A 403 1555 1555 2.31 LINK O1B APR A 401 MG MG A 403 1555 1555 2.43 LINK MG MG A 402 O HOH A 549 1555 1555 2.56 LINK MG MG A 402 O HOH A 562 1555 1555 2.28 LINK MG MG A 403 O HOH A 605 1555 1555 2.45 LINK MG MG A 403 O HOH A 613 1555 1555 2.47 LINK O GLY B 59 MG MG B 403 1555 1555 2.90 LINK OE2 GLU B 80 MG MG B 402 1555 1555 2.27 LINK OE2 GLU B 80 MG MG B 403 1555 1555 2.39 LINK OE1BGLU B 136 MG MG B 402 1555 1555 2.72 LINK O2B APR B 401 MG MG B 402 1555 1555 2.26 LINK O1A APR B 401 MG MG B 403 1555 1555 2.61 LINK MG MG B 402 O HOH B 553 1555 1555 2.67 LINK MG MG B 403 O HOH B 587 1555 1555 2.86 SITE 1 AC1 25 VAL A 22 HIS A 24 ARG A 50 GLY A 59 SITE 2 AC1 25 GLY A 60 PHE A 61 GLU A 76 GLU A 80 SITE 3 AC1 25 ALA A 108 GLU A 136 ILE A 164 SER A 166 SITE 4 AC1 25 ALA A 167 GLN A 170 MG A 402 MG A 403 SITE 5 AC1 25 HOH A 501 HOH A 506 HOH A 521 HOH A 526 SITE 6 AC1 25 HOH A 545 HOH A 608 HOH A 609 HOH A 613 SITE 7 AC1 25 PHE B 36 SITE 1 AC2 7 GLU A 76 GLU A 80 GLU A 136 APR A 401 SITE 2 AC2 7 MG A 403 HOH A 549 HOH A 562 SITE 1 AC3 6 GLY A 59 GLU A 80 APR A 401 MG A 402 SITE 2 AC3 6 HOH A 605 HOH A 613 SITE 1 AC4 1 LEU A 13 SITE 1 AC5 16 HIS B 24 ARG B 50 PHE B 51 GLY B 60 SITE 2 AC5 16 PHE B 61 GLU B 76 GLU B 80 ALA B 108 SITE 3 AC5 16 GLU B 136 ILE B 164 SER B 166 GLN B 170 SITE 4 AC5 16 MG B 402 MG B 403 HOH B 549 HOH B 587 SITE 1 AC6 6 GLU B 76 GLU B 80 ASP B 132 GLU B 136 SITE 2 AC6 6 APR B 401 HOH B 553 SITE 1 AC7 4 GLY B 59 GLU B 80 APR B 401 HOH B 587 SITE 1 AC8 6 GLY B 82 GLU B 83 ALA B 84 GLY B 126 SITE 2 AC8 6 ARG B 129 HOH B 511 SITE 1 AC9 9 PRO B 30 ARG B 114 LEU B 115 THR B 116 SITE 2 AC9 9 LEU B 117 HOH B 506 HOH B 533 HOH B 539 SITE 3 AC9 9 HOH B 583 CRYST1 113.755 46.319 74.238 90.00 107.65 90.00 C 1 2 1 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 0.008791 0.000000 0.002798 0.00000 SCALE2 0.000000 0.021589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014136 0.00000