PDB Short entry for 4HVY HEADER HYDROLASE 07-NOV-12 4HVY TITLE A THERMOSTABLE VARIANT OF HUMAN NUDT18 NUDIX DOMAIN OBTAINED BY HOT TITLE 2 COLONY FILTRATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 18; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUDIX HYDROLASE DOMAIN CONTAINING RESIDUES 26-179; COMPND 5 SYNONYM: NUDIX MOTIF 18; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 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: NUDT18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3) KEYWDS HYDROLASE, THERMOSTABILITY, DIRECTED EVOLUTION, HOT-COFI, HOT COLONY KEYWDS 2 FILTRATION EXPDTA X-RAY DIFFRACTION AUTHOR I.ASIAL,Y.X.CHENG,H.ENGMAN,B.WU,M.DOLLHOPF,P.NORDLUND,T.CORNVIK REVDAT 2 28-FEB-24 4HVY 1 REMARK SEQADV LINK REVDAT 1 01-JAN-14 4HVY 0 JRNL AUTH I.ASIAL,Y.X.CHENG,H.ENGMAN,M.DOLLHOPF,B.WU,P.NORDLUND, JRNL AUTH 2 T.CORNVIK JRNL TITL ENGINEERING PROTEIN THERMOSTABILITY USING A GENERIC JRNL TITL 2 ACTIVITY-INDEPENDENT BIOPHYSICAL SCREEN INSIDE THE CELL. JRNL REF NAT COMMUN V. 4 2901 2013 JRNL REFN ESSN 2041-1723 JRNL PMID 24352381 JRNL DOI 10.1038/NCOMMS3901 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 26681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1341 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.5292 - 3.1443 0.86 2360 115 0.1734 0.1985 REMARK 3 2 3.1443 - 2.4962 1.00 2603 133 0.1737 0.2152 REMARK 3 3 2.4962 - 2.1808 1.00 2588 133 0.1444 0.2019 REMARK 3 4 2.1808 - 1.9814 1.00 2547 164 0.1342 0.2056 REMARK 3 5 1.9814 - 1.8394 1.00 2543 141 0.1501 0.2255 REMARK 3 6 1.8394 - 1.7310 1.00 2548 129 0.1545 0.2159 REMARK 3 7 1.7310 - 1.6443 1.00 2527 141 0.1743 0.2362 REMARK 3 8 1.6443 - 1.5727 1.00 2555 111 0.1854 0.2078 REMARK 3 9 1.5727 - 1.5122 1.00 2533 133 0.2050 0.2472 REMARK 3 10 1.5122 - 1.4600 1.00 2536 141 0.2648 0.3061 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1239 REMARK 3 ANGLE : 1.147 1723 REMARK 3 CHIRALITY : 0.075 200 REMARK 3 PLANARITY : 0.005 222 REMARK 3 DIHEDRAL : 12.430 494 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL. REMARK 200 OPTICS : RH COATED REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 32.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.6 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-SODIUM CITRATE, 3.2M AMMONIUM REMARK 280 SULFATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 45.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 45.10000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.51500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.75750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.10000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.27250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 56.27250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.10000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.75750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 45.10000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.51500 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 45.10000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 37.51500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 45.10000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 56.27250 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 18.75750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 45.10000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 18.75750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 56.27250 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 45.10000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 45.10000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 37.51500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -275.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 406 LIES ON A SPECIAL POSITION. 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 25 REMARK 465 SER A 26 REMARK 465 ALA A 27 REMARK 465 PRO A 28 REMARK 465 ALA A 29 REMARK 465 GLY A 30 REMARK 465 GLU A 31 REMARK 465 PRO A 32 REMARK 465 PRO A 33 REMARK 465 ALA A 34 REMARK 465 PRO A 35 REMARK 465 VAL A 36 REMARK 465 ARG A 37 REMARK 465 LEU A 38 REMARK 465 ARG A 174 REMARK 465 HIS A 175 REMARK 465 PRO A 176 REMARK 465 LEU A 177 REMARK 465 ILE A 178 REMARK 465 LEU A 179 REMARK 465 ALA A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 39 NE CZ NH1 NH2 REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 93 CE NZ REMARK 470 ARG A 123 CD NE CZ NH1 NH2 REMARK 470 GLN A 171 CG CD OE1 NE2 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 GLN A 141 173.31 178.25 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 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 48 O REMARK 620 2 LEU A 58 O 125.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 89 OE1 REMARK 620 2 HOH A 324 O 130.7 REMARK 620 3 HOH A 444 O 124.4 70.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 210 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GG6 RELATED DB: PDB REMARK 900 HUMAN NUDT18 NUDIX DOMAIN, WILD-TYPE. DBREF 4HVY A 26 179 UNP Q6ZVK8 NUD18_HUMAN 26 179 SEQADV 4HVY MET A 25 UNP Q6ZVK8 INITIATING METHIONINE SEQADV 4HVY MET A 45 UNP Q6ZVK8 VAL 45 ENGINEERED MUTATION SEQADV 4HVY VAL A 91 UNP Q6ZVK8 GLU 91 ENGINEERED MUTATION SEQADV 4HVY ALA A 180 UNP Q6ZVK8 EXPRESSION TAG SEQADV 4HVY HIS A 181 UNP Q6ZVK8 EXPRESSION TAG SEQADV 4HVY HIS A 182 UNP Q6ZVK8 EXPRESSION TAG SEQADV 4HVY HIS A 183 UNP Q6ZVK8 EXPRESSION TAG SEQADV 4HVY HIS A 184 UNP Q6ZVK8 EXPRESSION TAG SEQADV 4HVY HIS A 185 UNP Q6ZVK8 EXPRESSION TAG SEQADV 4HVY HIS A 186 UNP Q6ZVK8 EXPRESSION TAG SEQRES 1 A 162 MET SER ALA PRO ALA GLY GLU PRO PRO ALA PRO VAL ARG SEQRES 2 A 162 LEU ARG LYS ASN VAL CYS TYR MET VAL LEU ALA VAL PHE SEQRES 3 A 162 LEU SER GLU GLN ASP GLU VAL LEU LEU ILE GLN GLU ALA SEQRES 4 A 162 LYS ARG GLU CYS ARG GLY SER TRP TYR LEU PRO ALA GLY SEQRES 5 A 162 ARG MET GLU PRO GLY GLU THR ILE VAL GLU ALA LEU GLN SEQRES 6 A 162 ARG VAL VAL LYS GLU GLU ALA GLY LEU HIS CYS GLU PRO SEQRES 7 A 162 GLU THR LEU LEU SER VAL GLU GLU ARG GLY PRO SER TRP SEQRES 8 A 162 VAL ARG PHE VAL PHE LEU ALA ARG PRO THR GLY GLY ILE SEQRES 9 A 162 LEU LYS THR SER LYS GLU ALA ASP ALA GLU SER LEU GLN SEQRES 10 A 162 ALA ALA TRP TYR PRO ARG THR SER LEU PRO THR PRO LEU SEQRES 11 A 162 ARG ALA HIS ASP ILE LEU HIS LEU VAL GLU LEU ALA ALA SEQRES 12 A 162 GLN TYR ARG GLN GLN ALA ARG HIS PRO LEU ILE LEU ALA SEQRES 13 A 162 HIS HIS HIS HIS HIS HIS HET GOL A 201 6 HET MG A 202 1 HET MG A 203 1 HET SO4 A 204 5 HET NA A 205 1 HET MG A 206 1 HET NA A 207 1 HET NA A 208 1 HET NA A 209 1 HET GOL A 210 6 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 3 MG 3(MG 2+) FORMUL 5 SO4 O4 S 2- FORMUL 6 NA 4(NA 1+) FORMUL 12 HOH *170(H2 O) HELIX 1 1 LYS A 64 ARG A 68 5 5 HELIX 2 2 THR A 83 GLY A 97 1 15 HELIX 3 3 THR A 131 ALA A 135 5 5 HELIX 4 4 HIS A 157 ALA A 173 1 17 SHEET 1 A 4 ALA A 75 ARG A 77 0 SHEET 2 A 4 CYS A 43 VAL A 49 -1 N VAL A 46 O GLY A 76 SHEET 3 A 4 TRP A 115 GLY A 127 1 O PHE A 120 N VAL A 49 SHEET 4 A 4 LEU A 98 GLY A 112 -1 N GLU A 103 O LEU A 121 SHEET 1 B 3 TRP A 71 TYR A 72 0 SHEET 2 B 3 GLU A 56 GLN A 61 -1 N ILE A 60 O TYR A 72 SHEET 3 B 3 GLN A 141 PRO A 146 -1 O TYR A 145 N VAL A 57 LINK O ALA A 48 MG MG A 203 1555 1555 2.95 LINK O LEU A 58 MG MG A 203 1555 1555 2.70 LINK OE1 GLN A 89 NA NA A 205 1555 1555 2.76 LINK MG MG A 202 O HOH A 433 1555 1555 2.86 LINK NA NA A 205 O HOH A 324 1555 1555 3.10 LINK NA NA A 205 O HOH A 444 1555 1555 2.46 CISPEP 1 THR A 152 PRO A 153 0 -10.21 SITE 1 AC1 3 LEU A 105 SER A 107 VAL A 108 SITE 1 AC2 3 TRP A 144 HOH A 358 HOH A 433 SITE 1 AC3 6 ALA A 48 VAL A 49 PHE A 50 LEU A 58 SITE 2 AC3 6 LEU A 73 PRO A 74 SITE 1 AC4 6 THR A 152 PRO A 153 LEU A 154 HIS A 157 SITE 2 AC4 6 HOH A 319 HOH A 470 SITE 1 AC5 3 GLN A 89 HOH A 324 HOH A 444 SITE 1 AC6 4 GLY A 112 PRO A 113 SER A 114 GLN A 172 SITE 1 AC7 2 HIS A 99 THR A 125 SITE 1 AC8 1 HIS A 157 SITE 1 AC9 6 HIS A 157 ASP A 158 HIS A 161 GLU A 164 SITE 2 AC9 6 HOH A 367 HOH A 436 CRYST1 90.200 90.200 75.030 90.00 90.00 90.00 I 41 2 2 16 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 0.011086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013328 0.00000