HEADER HYDROLASE, RNA BINDING PROTEIN 30-MAY-20 6X7V TITLE CRYSTAL STRUCTURE OF THE HUMAN NUDIX HYDROLASE NUDT16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: U8 SNORNA-DECAPPING ENZYME; COMPND 3 CHAIN: A, B, C, D; 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 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NUDIX, HYDROLASE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.HAMILTON,L.TONG REVDAT 3 18-OCT-23 6X7V 1 LINK REVDAT 2 22-JUL-20 6X7V 1 JRNL REVDAT 1 01-JUL-20 6X7V 0 JRNL AUTH S.SHARMA,E.GRUDZIEN-NOGALSKA,K.HAMILTON,X.JIAO,J.YANG, JRNL AUTH 2 L.TONG,M.KILEDJIAN JRNL TITL MAMMALIAN NUDIX PROTEINS CLEAVE NUCLEOTIDE METABOLITE CAPS JRNL TITL 2 ON RNAS. JRNL REF NUCLEIC ACIDS RES. V. 48 6788 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32432673 JRNL DOI 10.1093/NAR/GKAA402 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 28837 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1442 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 46.2800 - 4.9600 0.95 2850 150 0.1990 0.2414 REMARK 3 2 4.9600 - 3.9400 0.98 2781 147 0.1720 0.2280 REMARK 3 3 3.9400 - 3.4400 0.97 2724 144 0.2229 0.2993 REMARK 3 4 3.4400 - 3.1300 0.99 2776 145 0.2399 0.3328 REMARK 3 5 3.1300 - 2.9000 0.99 2748 145 0.2677 0.3690 REMARK 3 6 2.9000 - 2.7300 0.98 2722 143 0.2745 0.3621 REMARK 3 7 2.7300 - 2.6000 0.99 2741 144 0.2784 0.3357 REMARK 3 8 2.6000 - 2.4800 0.99 2739 144 0.2965 0.3360 REMARK 3 9 2.4800 - 2.3900 1.00 2740 144 0.3355 0.3661 REMARK 3 10 2.3900 - 2.3000 0.92 2574 136 0.3760 0.4629 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.92 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6X7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20180808 REMARK 200 DATA SCALING SOFTWARE : XDS 20180808 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28854 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.76500 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: PHASER 2.8.2 REMARK 200 STARTING MODEL: 3MGM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 20% (W/V) PEG REMARK 280 3350, 0.1 M MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 42.84300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.49500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.96100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.49500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.84300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.96100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 2840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 GLY A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 LEU A 7 REMARK 465 GLU A 8 REMARK 465 LEU A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 ALA A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 GLY A 18 REMARK 465 TRP A 19 REMARK 465 GLY A 101 REMARK 465 SER A 102 REMARK 465 GLY A 103 REMARK 465 PRO A 104 REMARK 465 LEU A 181 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 ALA B 4 REMARK 465 ARG B 5 REMARK 465 ARG B 6 REMARK 465 LEU B 7 REMARK 465 GLU B 8 REMARK 465 LEU B 9 REMARK 465 GLY B 10 REMARK 465 GLU B 11 REMARK 465 ALA B 12 REMARK 465 LEU B 13 REMARK 465 ALA B 14 REMARK 465 LEU B 15 REMARK 465 GLY B 16 REMARK 465 SER B 17 REMARK 465 THR B 64 REMARK 465 GLN B 65 REMARK 465 GLY B 101 REMARK 465 SER B 102 REMARK 465 GLY B 103 REMARK 465 LEU B 181 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 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLY C 3 REMARK 465 ALA C 4 REMARK 465 ARG C 5 REMARK 465 ARG C 6 REMARK 465 LEU C 7 REMARK 465 GLU C 8 REMARK 465 LEU C 9 REMARK 465 GLY C 10 REMARK 465 GLU C 11 REMARK 465 ALA C 12 REMARK 465 LEU C 13 REMARK 465 ALA C 14 REMARK 465 LEU C 15 REMARK 465 GLY C 16 REMARK 465 SER C 17 REMARK 465 GLY C 18 REMARK 465 TRP C 19 REMARK 465 SER C 102 REMARK 465 GLY C 103 REMARK 465 LEU C 181 REMARK 465 GLN C 182 REMARK 465 SER C 183 REMARK 465 GLY C 184 REMARK 465 SER C 185 REMARK 465 ILE C 186 REMARK 465 SER C 187 REMARK 465 GLY C 188 REMARK 465 LEU C 189 REMARK 465 LYS C 190 REMARK 465 ILE C 191 REMARK 465 PRO C 192 REMARK 465 ALA C 193 REMARK 465 HIS C 194 REMARK 465 HIS C 195 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 GLY D 3 REMARK 465 ALA D 4 REMARK 465 ARG D 5 REMARK 465 ARG D 6 REMARK 465 LEU D 7 REMARK 465 GLU D 8 REMARK 465 LEU D 9 REMARK 465 GLY D 101 REMARK 465 SER D 102 REMARK 465 GLY D 103 REMARK 465 LEU D 181 REMARK 465 GLN D 182 REMARK 465 SER D 183 REMARK 465 GLY D 184 REMARK 465 SER D 185 REMARK 465 ILE D 186 REMARK 465 SER D 187 REMARK 465 GLY D 188 REMARK 465 LEU D 189 REMARK 465 LYS D 190 REMARK 465 ILE D 191 REMARK 465 PRO D 192 REMARK 465 ALA D 193 REMARK 465 HIS D 194 REMARK 465 HIS D 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 O HOH C 202 O HOH C 218 1.93 REMARK 500 O GLY D 134 O HOH D 301 1.99 REMARK 500 O LEU D 140 O HOH D 302 2.10 REMARK 500 ND1 HIS D 133 O HOH D 303 2.12 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 OE1 GLU B 169 NH1 ARG D 20 3546 2.16 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 ALA D 14 N - CA - C ANGL. DEV. = -24.5 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 PHE A 36 14.52 56.98 REMARK 500 ARG A 38 -30.17 -133.62 REMARK 500 ARG A 67 61.41 -116.95 REMARK 500 SER A 68 127.02 -177.49 REMARK 500 ARG A 96 -40.68 -138.44 REMARK 500 LEU A 135 -84.32 -118.66 REMARK 500 VAL A 152 -40.16 -140.08 REMARK 500 ARG B 96 -81.74 -88.44 REMARK 500 THR B 128 2.21 -63.07 REMARK 500 ARG B 129 30.20 -141.86 REMARK 500 LEU B 135 -83.44 -99.30 REMARK 500 ASP B 150 3.14 -66.60 REMARK 500 ASN B 161 -176.86 -68.24 REMARK 500 SER B 166 -18.71 85.02 REMARK 500 ARG C 38 -35.83 -138.93 REMARK 500 LEU C 135 -84.12 -117.46 REMARK 500 ASP C 150 13.23 -65.78 REMARK 500 VAL C 152 -59.52 -124.37 REMARK 500 ASP C 177 8.49 -62.56 REMARK 500 ALA D 12 -6.98 -57.84 REMARK 500 LEU D 13 43.43 -98.99 REMARK 500 ARG D 38 -20.76 -152.98 REMARK 500 ASP D 63 -167.41 -108.51 REMARK 500 ARG D 67 -76.32 -48.90 REMARK 500 ALA D 87 8.76 -65.30 REMARK 500 LEU D 135 -81.69 -127.89 REMARK 500 VAL D 152 -41.45 -130.46 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 NE2 REMARK 620 2 GLU A 173 OE2 116.4 REMARK 620 3 HIS C 99 NE2 116.6 31.6 REMARK 620 4 GLU C 173 OE1 114.8 35.2 3.8 REMARK 620 5 GLU C 173 OE2 115.7 32.7 1.4 2.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6X7U RELATED DB: PDB DBREF 6X7V A 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 DBREF 6X7V B 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 DBREF 6X7V C 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 DBREF 6X7V D 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 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 ALA 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 ALA 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 SEQRES 1 C 195 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 C 195 ALA LEU GLY SER GLY TRP ARG HIS ALA CYS HIS ALA LEU SEQRES 3 C 195 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 C 195 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 C 195 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 C 195 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 C 195 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 C 195 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 C 195 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 C 195 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 C 195 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 C 195 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 C 195 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 C 195 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 C 195 SER GLY SER ILE SER GLY LEU LYS ILE PRO ALA HIS HIS SEQRES 1 D 195 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 D 195 ALA LEU GLY SER GLY TRP ARG HIS ALA CYS HIS ALA LEU SEQRES 3 D 195 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 D 195 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 D 195 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 D 195 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 D 195 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 D 195 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 D 195 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 D 195 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 D 195 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 D 195 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 D 195 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 D 195 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 D 195 SER GLY SER ILE SER GLY LEU LYS ILE PRO ALA HIS HIS HET MN A 201 1 HET CL D 201 1 HETNAM MN MANGANESE (II) ION HETNAM CL CHLORIDE ION FORMUL 5 MN MN 2+ FORMUL 6 CL CL 1- FORMUL 7 HOH *54(H2 O) HELIX 1 AA1 PHE A 36 ARG A 38 5 3 HELIX 2 AA2 SER A 68 GLY A 82 1 15 HELIX 3 AA3 GLU A 83 PHE A 88 5 6 HELIX 4 AA4 GLU A 91 THR A 93 5 3 HELIX 5 AA5 THR A 116 THR A 128 1 13 HELIX 6 AA6 GLY A 154 LEU A 159 1 6 HELIX 7 AA7 SER A 166 LEU A 178 1 13 HELIX 8 AA8 PHE B 36 ARG B 38 5 3 HELIX 9 AA9 SER B 68 GLY B 82 1 15 HELIX 10 AB1 GLU B 83 PHE B 88 5 6 HELIX 11 AB2 GLU B 91 THR B 93 5 3 HELIX 12 AB3 THR B 116 THR B 128 1 13 HELIX 13 AB4 GLY B 154 LEU B 159 1 6 HELIX 14 AB5 SER B 166 ASP B 177 1 12 HELIX 15 AB6 PHE C 36 ARG C 38 5 3 HELIX 16 AB7 SER C 68 GLY C 82 1 15 HELIX 17 AB8 ALA C 84 PHE C 88 5 5 HELIX 18 AB9 GLU C 91 THR C 93 5 3 HELIX 19 AC1 THR C 116 ALA C 127 1 12 HELIX 20 AC2 THR C 128 ALA C 130 5 3 HELIX 21 AC3 GLY C 154 GLU C 160 1 7 HELIX 22 AC4 SER C 166 ASP C 177 1 12 HELIX 23 AC5 SER D 68 GLY D 82 1 15 HELIX 24 AC6 GLU D 83 PHE D 88 5 6 HELIX 25 AC7 GLU D 91 THR D 93 5 3 HELIX 26 AC8 THR D 116 ALA D 127 1 12 HELIX 27 AC9 THR D 128 ALA D 130 5 3 HELIX 28 AD1 GLY D 154 LEU D 159 1 6 HELIX 29 AD2 SER D 166 LEU D 178 1 13 SHEET 1 AA1 5 LEU A 55 GLY A 56 0 SHEET 2 AA1 5 TYR A 43 ARG A 50 -1 N GLN A 48 O GLY A 56 SHEET 3 AA1 5 HIS A 21 PRO A 30 -1 N ALA A 29 O ALA A 44 SHEET 4 AA1 5 VAL A 107 ARG A 114 1 O HIS A 109 N ALA A 22 SHEET 5 AA1 5 TYR A 95 HIS A 99 -1 N SER A 97 O PHE A 110 SHEET 1 AA2 4 GLY A 59 PHE A 61 0 SHEET 2 AA2 4 HIS A 21 PRO A 30 -1 N CYS A 23 O GLY A 60 SHEET 3 AA2 4 TYR A 43 ARG A 50 -1 O ALA A 44 N ALA A 29 SHEET 4 AA2 4 VAL A 137 ARG A 142 -1 O VAL A 141 N MET A 47 SHEET 1 AA3 2 MET A 34 LEU A 35 0 SHEET 2 AA3 2 ILE A 39 PRO A 40 -1 O ILE A 39 N LEU A 35 SHEET 1 AA4 5 LEU B 55 GLY B 56 0 SHEET 2 AA4 5 TYR B 43 ARG B 50 -1 N GLN B 48 O GLY B 56 SHEET 3 AA4 5 ARG B 20 PRO B 30 -1 N ALA B 29 O ALA B 44 SHEET 4 AA4 5 VAL B 106 ARG B 114 1 O VAL B 107 N ALA B 22 SHEET 5 AA4 5 TYR B 95 HIS B 99 -1 N SER B 97 O PHE B 110 SHEET 1 AA5 4 GLY B 59 PHE B 61 0 SHEET 2 AA5 4 ARG B 20 PRO B 30 -1 N CYS B 23 O GLY B 60 SHEET 3 AA5 4 TYR B 43 ARG B 50 -1 O ALA B 44 N ALA B 29 SHEET 4 AA5 4 VAL B 137 ARG B 142 -1 O LEU B 138 N MET B 49 SHEET 1 AA6 2 MET B 34 LEU B 35 0 SHEET 2 AA6 2 ILE B 39 PRO B 40 -1 O ILE B 39 N LEU B 35 SHEET 1 AA7 5 LEU C 55 GLY C 56 0 SHEET 2 AA7 5 TYR C 43 ARG C 50 -1 N GLN C 48 O GLY C 56 SHEET 3 AA7 5 HIS C 21 PRO C 30 -1 N ALA C 29 O ALA C 44 SHEET 4 AA7 5 VAL C 106 ARG C 114 1 O HIS C 109 N ALA C 22 SHEET 5 AA7 5 TYR C 95 GLY C 101 -1 N GLY C 101 O VAL C 106 SHEET 1 AA8 4 GLY C 59 PHE C 61 0 SHEET 2 AA8 4 HIS C 21 PRO C 30 -1 N CYS C 23 O GLY C 60 SHEET 3 AA8 4 TYR C 43 ARG C 50 -1 O ALA C 44 N ALA C 29 SHEET 4 AA8 4 VAL C 137 ARG C 142 -1 O GLY C 139 N MET C 49 SHEET 1 AA9 2 MET C 34 LEU C 35 0 SHEET 2 AA9 2 ILE C 39 PRO C 40 -1 O ILE C 39 N LEU C 35 SHEET 1 AB1 5 LEU D 55 GLY D 56 0 SHEET 2 AB1 5 TYR D 43 ARG D 50 -1 N GLN D 48 O GLY D 56 SHEET 3 AB1 5 ARG D 20 PRO D 30 -1 N ALA D 29 O ALA D 44 SHEET 4 AB1 5 VAL D 106 ARG D 114 1 O TYR D 111 N LEU D 26 SHEET 5 AB1 5 TYR D 95 HIS D 99 -1 N SER D 97 O PHE D 110 SHEET 1 AB2 4 GLY D 59 VAL D 62 0 SHEET 2 AB2 4 ARG D 20 PRO D 30 -1 N CYS D 23 O GLY D 60 SHEET 3 AB2 4 TYR D 43 ARG D 50 -1 O ALA D 44 N ALA D 29 SHEET 4 AB2 4 VAL D 137 ARG D 142 -1 O LEU D 138 N MET D 49 SHEET 1 AB3 2 MET D 34 LEU D 35 0 SHEET 2 AB3 2 ILE D 39 PRO D 40 -1 O ILE D 39 N LEU D 35 LINK NE2 HIS A 99 MN MN A 201 1555 1555 2.42 LINK OE2 GLU A 173 MN MN A 201 1555 1555 2.05 LINK MN MN A 201 NE2 HIS C 99 2555 1555 2.05 LINK MN MN A 201 OE1 GLU C 173 2555 1555 2.73 LINK MN MN A 201 OE2 GLU C 173 2555 1555 2.36 SITE 1 AC1 4 HIS A 99 GLU A 173 HIS C 99 GLU C 173 SITE 1 AC2 2 MET A 34 ARG D 149 CRYST1 85.686 137.922 54.990 90.00 90.00 90.00 P 21 21 21 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 0.011671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007250 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018185 0.00000