HEADER HYDROLASE 22-MAR-16 5IW5 TITLE CRYSTAL STRUCTURE OF E. COLI NUDC IN COMPLEX WITH NMN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH PYROPHOSPHATASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: NUDC; COMPND 5 EC: 3.6.1.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI B354; SOURCE 3 ORGANISM_TAXID: 550677; SOURCE 4 STRAIN: B354; SOURCE 5 GENE: NUDC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-SUMO KEYWDS NMN, RNA, CAPPING, NUDIX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LI,J.DU,D.J.PATEL REVDAT 4 08-NOV-23 5IW5 1 REMARK REVDAT 3 07-SEP-16 5IW5 1 JRNL REVDAT 2 20-JUL-16 5IW5 1 JRNL REVDAT 1 13-JUL-16 5IW5 0 JRNL AUTH K.HOFER,S.LI,F.ABELE,J.FRINDERT,J.SCHLOTTHAUER,J.GRAWENHOFF, JRNL AUTH 2 J.DU,D.J.PATEL,A.JASCHKE JRNL TITL STRUCTURE AND FUNCTION OF THE BACTERIAL DECAPPING ENZYME JRNL TITL 2 NUDC JRNL REF NAT.CHEM.BIOL. V. 12 730 2016 JRNL REFN ESSN 1552-4469 JRNL PMID 27428510 JRNL DOI 10.1038/NCHEMBIO.2132 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 770 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 46.5526 - 4.6158 1.00 2996 162 0.1863 0.2096 REMARK 3 2 4.6158 - 3.6642 1.00 2942 142 0.1597 0.1852 REMARK 3 3 3.6642 - 3.2011 0.99 2889 174 0.2029 0.2872 REMARK 3 4 3.2011 - 2.9085 0.99 2896 140 0.2396 0.2767 REMARK 3 5 2.9085 - 2.7000 0.99 2889 152 0.2685 0.3083 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.014 4280 REMARK 3 ANGLE : 1.484 5822 REMARK 3 CHIRALITY : 0.229 616 REMARK 3 PLANARITY : 0.005 752 REMARK 3 DIHEDRAL : 19.013 1582 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 145.4658 26.0445 25.2093 REMARK 3 T TENSOR REMARK 3 T11: 0.3273 T22: 0.1662 REMARK 3 T33: 0.2117 T12: 0.0313 REMARK 3 T13: 0.0491 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.8303 L22: 2.7819 REMARK 3 L33: 5.5127 L12: 0.7764 REMARK 3 L13: 2.0106 L23: -0.1007 REMARK 3 S TENSOR REMARK 3 S11: 0.0409 S12: 0.1953 S13: 0.0189 REMARK 3 S21: 0.3126 S22: 0.0184 S23: -0.0769 REMARK 3 S31: -0.4108 S32: -0.0682 S33: -0.0590 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 117 THROUGH 257 ) REMARK 3 ORIGIN FOR THE GROUP (A): 140.3068 3.0562 43.5937 REMARK 3 T TENSOR REMARK 3 T11: 0.3616 T22: 0.3875 REMARK 3 T33: 0.2475 T12: 0.0846 REMARK 3 T13: 0.0472 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 2.7878 L22: 2.6280 REMARK 3 L33: 3.5669 L12: 1.1822 REMARK 3 L13: 0.0565 L23: 0.2712 REMARK 3 S TENSOR REMARK 3 S11: -0.0633 S12: -0.0486 S13: 0.0454 REMARK 3 S21: 0.2423 S22: -0.0109 S23: 0.5494 REMARK 3 S31: -0.0520 S32: -0.7059 S33: 0.0459 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 146.2716 50.3659 16.4623 REMARK 3 T TENSOR REMARK 3 T11: 0.1830 T22: 0.2103 REMARK 3 T33: 0.2092 T12: -0.0226 REMARK 3 T13: -0.0141 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 2.5252 L22: 2.6980 REMARK 3 L33: 3.7671 L12: -0.8041 REMARK 3 L13: -1.6592 L23: 0.1603 REMARK 3 S TENSOR REMARK 3 S11: 0.0239 S12: -0.2361 S13: -0.1878 REMARK 3 S21: 0.3021 S22: -0.0752 S23: 0.0186 REMARK 3 S31: 0.1958 S32: 0.1144 S33: 0.0207 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 257 ) REMARK 3 ORIGIN FOR THE GROUP (A): 145.0250 73.6647 -2.9470 REMARK 3 T TENSOR REMARK 3 T11: 0.1380 T22: 0.2276 REMARK 3 T33: 0.1914 T12: -0.0106 REMARK 3 T13: 0.0031 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.4832 L22: 2.1476 REMARK 3 L33: 1.2978 L12: -1.3157 REMARK 3 L13: -0.2980 L23: 0.1350 REMARK 3 S TENSOR REMARK 3 S11: 0.1200 S12: 0.1730 S13: -0.1316 REMARK 3 S21: -0.1755 S22: -0.1533 S23: 0.2356 REMARK 3 S31: -0.1073 S32: -0.0367 S33: 0.0320 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 5IW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15413 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.78900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1VK6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M LICL2, 0.1 M HEPES, 10% PEG6000, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 52.43150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.10900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.43150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.10900 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 307.03228 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 86.54773 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: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 -1.000000 0.000000 0.000000 314.58900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 B 403 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 SER B 0 REMARK 465 MET B 1 REMARK 465 SER A 0 REMARK 465 ARG A 148 REMARK 465 HIS A 149 REMARK 465 ARG A 150 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 LYS B 7 CG CD CE NZ REMARK 470 LYS B 218 CG CD CE NZ 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 ND1 HIS B 17 CD GLN B 60 1.84 REMARK 500 CE1 HIS B 17 NE2 GLN B 60 1.90 REMARK 500 OD2 ASP A 139 NH1 ARG A 227 2.06 REMARK 500 OD1 ASP A 216 NZ LYS A 218 2.10 REMARK 500 NH2 ARG A 3 OD2 ASP A 9 2.14 REMARK 500 O VAL B 175 OG SER B 179 2.17 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 NH2 ARG B 93 OE2 GLU B 121 2856 2.06 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 GLN B 19 1.05 84.43 REMARK 500 LYS B 25 18.29 56.26 REMARK 500 ASP B 75 141.46 -170.55 REMARK 500 GLU B 111 -168.70 -114.97 REMARK 500 TRP B 112 69.53 -110.20 REMARK 500 ASP B 138 -116.61 58.32 REMARK 500 ARG B 150 36.02 -161.57 REMARK 500 THR B 155 -166.43 -121.54 REMARK 500 ASP A 2 -178.48 58.93 REMARK 500 ARG A 3 170.04 172.50 REMARK 500 LEU A 8 -9.59 86.50 REMARK 500 GLN A 19 -1.00 67.50 REMARK 500 SER A 117 -7.47 82.53 REMARK 500 ASP A 138 -104.33 55.66 REMARK 500 THR A 190 -176.53 -173.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 475 DISTANCE = 6.19 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 98 SG REMARK 620 2 CYS B 101 SG 92.0 REMARK 620 3 CYS B 116 SG 116.5 134.9 REMARK 620 4 CYS B 119 SG 122.7 86.3 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 98 SG REMARK 620 2 CYS A 116 SG 115.1 REMARK 620 3 CYS A 119 SG 119.7 111.8 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 ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NMN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NMN A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IW4 RELATED DB: PDB DBREF 5IW5 B 1 257 UNP D6JHV3 D6JHV3_ECOLX 1 257 DBREF 5IW5 A 1 257 UNP D6JHV3 D6JHV3_ECOLX 1 257 SEQADV 5IW5 SER B 0 UNP D6JHV3 EXPRESSION TAG SEQADV 5IW5 SER A 0 UNP D6JHV3 EXPRESSION TAG SEQRES 1 B 258 SER MET ASP ARG ILE ILE GLU LYS LEU ASP HIS GLY TRP SEQRES 2 B 258 TRP VAL VAL SER HIS GLU GLN LYS LEU TRP LEU PRO LYS SEQRES 3 B 258 GLY GLU LEU PRO TYR GLY GLU ALA ALA ASN PHE ASP LEU SEQRES 4 B 258 VAL GLY GLN ARG ALA LEU GLN ILE GLY GLU TRP GLN GLY SEQRES 5 B 258 GLU PRO VAL TRP LEU VAL GLN GLN GLN ARG ARG HIS ASP SEQRES 6 B 258 MET GLY SER VAL ARG GLN VAL ILE ASP LEU ASP VAL GLY SEQRES 7 B 258 LEU PHE GLN LEU ALA GLY ARG GLY VAL GLN LEU ALA GLU SEQRES 8 B 258 PHE TYR ARG SER HIS LYS TYR CYS GLY TYR CYS GLY HIS SEQRES 9 B 258 GLU MET TYR PRO SER LYS THR GLU TRP ALA MET LEU CYS SEQRES 10 B 258 SER HIS CYS ARG GLU ARG TYR TYR PRO GLN ILE ALA PRO SEQRES 11 B 258 CYS ILE ILE VAL ALA ILE ARG ARG ASP ASP SER ILE LEU SEQRES 12 B 258 LEU ALA GLN HIS THR ARG HIS ARG ASN GLY VAL HIS THR SEQRES 13 B 258 VAL LEU ALA GLY PHE VAL GLU VAL GLY GLU THR LEU GLU SEQRES 14 B 258 GLN ALA VAL ALA ARG GLU VAL MET GLU GLU SER GLY ILE SEQRES 15 B 258 LYS VAL LYS ASN LEU ARG TYR VAL THR SER GLN PRO TRP SEQRES 16 B 258 PRO PHE PRO GLN SER LEU MET THR ALA PHE MET ALA GLU SEQRES 17 B 258 TYR ASP SER GLY ASP ILE VAL ILE ASP PRO LYS GLU LEU SEQRES 18 B 258 LEU GLU ALA ASN TRP TYR ARG TYR ASP ASP LEU PRO LEU SEQRES 19 B 258 LEU PRO PRO PRO GLY THR VAL ALA ARG ARG LEU ILE GLU SEQRES 20 B 258 ASP THR VAL ALA MET CYS ARG ALA GLU TYR GLU SEQRES 1 A 258 SER MET ASP ARG ILE ILE GLU LYS LEU ASP HIS GLY TRP SEQRES 2 A 258 TRP VAL VAL SER HIS GLU GLN LYS LEU TRP LEU PRO LYS SEQRES 3 A 258 GLY GLU LEU PRO TYR GLY GLU ALA ALA ASN PHE ASP LEU SEQRES 4 A 258 VAL GLY GLN ARG ALA LEU GLN ILE GLY GLU TRP GLN GLY SEQRES 5 A 258 GLU PRO VAL TRP LEU VAL GLN GLN GLN ARG ARG HIS ASP SEQRES 6 A 258 MET GLY SER VAL ARG GLN VAL ILE ASP LEU ASP VAL GLY SEQRES 7 A 258 LEU PHE GLN LEU ALA GLY ARG GLY VAL GLN LEU ALA GLU SEQRES 8 A 258 PHE TYR ARG SER HIS LYS TYR CYS GLY TYR CYS GLY HIS SEQRES 9 A 258 GLU MET TYR PRO SER LYS THR GLU TRP ALA MET LEU CYS SEQRES 10 A 258 SER HIS CYS ARG GLU ARG TYR TYR PRO GLN ILE ALA PRO SEQRES 11 A 258 CYS ILE ILE VAL ALA ILE ARG ARG ASP ASP SER ILE LEU SEQRES 12 A 258 LEU ALA GLN HIS THR ARG HIS ARG ASN GLY VAL HIS THR SEQRES 13 A 258 VAL LEU ALA GLY PHE VAL GLU VAL GLY GLU THR LEU GLU SEQRES 14 A 258 GLN ALA VAL ALA ARG GLU VAL MET GLU GLU SER GLY ILE SEQRES 15 A 258 LYS VAL LYS ASN LEU ARG TYR VAL THR SER GLN PRO TRP SEQRES 16 A 258 PRO PHE PRO GLN SER LEU MET THR ALA PHE MET ALA GLU SEQRES 17 A 258 TYR ASP SER GLY ASP ILE VAL ILE ASP PRO LYS GLU LEU SEQRES 18 A 258 LEU GLU ALA ASN TRP TYR ARG TYR ASP ASP LEU PRO LEU SEQRES 19 A 258 LEU PRO PRO PRO GLY THR VAL ALA ARG ARG LEU ILE GLU SEQRES 20 A 258 ASP THR VAL ALA MET CYS ARG ALA GLU TYR GLU HET ZN B 301 1 HET NMN B 302 22 HET ZN A 301 1 HET NMN A 302 22 HETNAM ZN ZINC ION HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NMN 2(C11 H16 N2 O8 P 1+) FORMUL 7 HOH *111(H2 O) HELIX 1 AA1 PRO B 24 GLU B 27 5 4 HELIX 2 AA2 ALA B 34 ASP B 37 5 4 HELIX 3 AA3 ASP B 75 HIS B 95 1 21 HELIX 4 AA4 THR B 166 GLY B 180 1 15 HELIX 5 AA5 THR B 239 GLU B 257 1 19 HELIX 6 AA6 PRO A 24 GLU A 27 5 4 HELIX 7 AA7 SER A 67 ILE A 72 5 6 HELIX 8 AA8 ASP A 75 SER A 94 1 20 HELIX 9 AA9 THR A 166 SER A 179 1 14 HELIX 10 AB1 THR A 239 GLU A 257 1 19 SHEET 1 AA1 5 ARG B 3 ILE B 4 0 SHEET 2 AA1 5 ARG B 42 TRP B 49 -1 O ALA B 43 N ARG B 3 SHEET 3 AA1 5 GLU B 52 VAL B 57 -1 O LEU B 56 N LEU B 44 SHEET 4 AA1 5 HIS B 10 HIS B 17 1 N VAL B 14 O TRP B 55 SHEET 5 AA1 5 TYR B 30 GLU B 32 -1 O GLY B 31 N GLY B 11 SHEET 1 AA2 6 ARG B 3 ILE B 4 0 SHEET 2 AA2 6 ARG B 42 TRP B 49 -1 O ALA B 43 N ARG B 3 SHEET 3 AA2 6 GLU B 52 VAL B 57 -1 O LEU B 56 N LEU B 44 SHEET 4 AA2 6 HIS B 10 HIS B 17 1 N VAL B 14 O TRP B 55 SHEET 5 AA2 6 LYS B 20 TRP B 22 -1 O TRP B 22 N VAL B 15 SHEET 6 AA2 6 MET B 65 GLY B 66 -1 O GLY B 66 N LEU B 21 SHEET 1 AA3 2 MET B 105 PRO B 107 0 SHEET 2 AA3 2 MET B 114 CYS B 116 -1 O LEU B 115 N TYR B 106 SHEET 1 AA4 4 LEU B 157 PHE B 160 0 SHEET 2 AA4 4 ALA B 128 ARG B 137 -1 N ILE B 131 O GLY B 159 SHEET 3 AA4 4 SER B 199 SER B 210 1 O TYR B 208 N ARG B 136 SHEET 4 AA4 4 LYS B 182 TRP B 194 -1 N THR B 190 O ALA B 203 SHEET 1 AA5 4 LEU B 157 PHE B 160 0 SHEET 2 AA5 4 ALA B 128 ARG B 137 -1 N ILE B 131 O GLY B 159 SHEET 3 AA5 4 SER B 140 HIS B 146 -1 O LEU B 142 N ILE B 135 SHEET 4 AA5 4 LEU B 220 ARG B 227 -1 O ASN B 224 N LEU B 143 SHEET 1 AA6 5 ARG A 3 ILE A 4 0 SHEET 2 AA6 5 ARG A 42 TRP A 49 -1 O ALA A 43 N ARG A 3 SHEET 3 AA6 5 GLU A 52 VAL A 57 -1 O LEU A 56 N LEU A 44 SHEET 4 AA6 5 HIS A 10 HIS A 17 1 N VAL A 14 O TRP A 55 SHEET 5 AA6 5 TYR A 30 GLU A 32 -1 O GLY A 31 N GLY A 11 SHEET 1 AA7 6 ARG A 3 ILE A 4 0 SHEET 2 AA7 6 ARG A 42 TRP A 49 -1 O ALA A 43 N ARG A 3 SHEET 3 AA7 6 GLU A 52 VAL A 57 -1 O LEU A 56 N LEU A 44 SHEET 4 AA7 6 HIS A 10 HIS A 17 1 N VAL A 14 O TRP A 55 SHEET 5 AA7 6 LYS A 20 TRP A 22 -1 O TRP A 22 N VAL A 15 SHEET 6 AA7 6 MET A 65 GLY A 66 -1 O GLY A 66 N LEU A 21 SHEET 1 AA8 3 TYR A 106 PRO A 107 0 SHEET 2 AA8 3 MET A 114 LEU A 115 -1 O LEU A 115 N TYR A 106 SHEET 3 AA8 3 ARG A 122 TYR A 123 -1 O TYR A 123 N MET A 114 SHEET 1 AA9 4 LEU A 157 PHE A 160 0 SHEET 2 AA9 4 ALA A 128 ARG A 137 -1 N VAL A 133 O LEU A 157 SHEET 3 AA9 4 SER A 199 SER A 210 1 O LEU A 200 N CYS A 130 SHEET 4 AA9 4 LYS A 182 TRP A 194 -1 N THR A 190 O ALA A 203 SHEET 1 AB1 4 LEU A 157 PHE A 160 0 SHEET 2 AB1 4 ALA A 128 ARG A 137 -1 N VAL A 133 O LEU A 157 SHEET 3 AB1 4 SER A 140 HIS A 146 -1 O SER A 140 N ARG A 137 SHEET 4 AB1 4 LEU A 220 ARG A 227 -1 O ASN A 224 N LEU A 143 LINK ND1 HIS B 17 NE2 GLN B 60 1555 1555 1.31 LINK SG CYS B 98 ZN ZN B 301 1555 1555 2.34 LINK SG CYS B 101 ZN ZN B 301 1555 1555 2.63 LINK SG CYS B 116 ZN ZN B 301 1555 1555 2.76 LINK SG CYS B 119 ZN ZN B 301 1555 1555 2.59 LINK SG CYS A 98 ZN ZN A 301 1555 1555 2.57 LINK SG CYS A 116 ZN ZN A 301 1555 1555 2.09 LINK SG CYS A 119 ZN ZN A 301 1555 1555 2.58 CISPEP 1 PHE B 196 PRO B 197 0 0.00 CISPEP 2 PHE A 196 PRO A 197 0 -6.11 SITE 1 AC1 4 CYS B 98 CYS B 101 CYS B 116 CYS B 119 SITE 1 AC2 11 ARG B 69 CYS B 130 TRP B 194 PRO B 197 SITE 2 AC2 11 SER B 199 MET B 201 PRO B 235 PRO B 236 SITE 3 AC2 11 THR B 239 VAL B 240 ALA B 241 SITE 1 AC3 4 CYS A 98 CYS A 101 CYS A 116 CYS A 119 SITE 1 AC4 10 ARG A 69 PHE A 160 TRP A 194 PRO A 197 SITE 2 AC4 10 SER A 199 MET A 201 PRO A 236 THR A 239 SITE 3 AC4 10 ALA A 241 HOH A 425 CRYST1 104.863 62.218 86.877 90.00 94.99 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 0.009536 0.000000 0.000832 0.00000 SCALE2 0.000000 0.016073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011554 0.00000