HEADER RNA BINDING PROTEIN 15-MAR-16 5ISY TITLE CRYSTAL STRUCTURE OF NUDIX FAMILY PROTEIN WITH NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH PYROPHOSPHATASE; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: N6-ADENOSINE-METHYLTRANSFERASE 70 KDA SUBUNIT, N6-ADENOSINE- COMPND 5 METHYLTRANSFERASE SUBUNIT METTL14; COMPND 6 EC: 3.6.1.22; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: NUDC, YJAD, B3996, JW5548; 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 KEYWDS NUDIX FAMILY, COMPLEX, NAD, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.ZHANG,Z.GUAN,T.ZOU,P.YIN REVDAT 2 08-NOV-23 5ISY 1 REMARK REVDAT 1 14-SEP-16 5ISY 0 JRNL AUTH D.ZHANG,Y.LIU,Q.WANG,Z.GUAN,J.WANG,J.LIU,T.ZOU,P.YIN JRNL TITL STRUCTURAL BASIS OF PROKARYOTIC NAD-RNA DECAPPING BY NUDC JRNL REF CELL RES. V. 26 1062 2016 JRNL REFN ISSN 1001-0602 JRNL PMID 27561816 JRNL DOI 10.1038/CR.2016.98 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1241 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 46.2987 - 4.8957 0.99 2813 140 0.1712 0.2152 REMARK 3 2 4.8957 - 3.8865 1.00 2672 154 0.1466 0.2030 REMARK 3 3 3.8865 - 3.3954 1.00 2666 128 0.1689 0.2307 REMARK 3 4 3.3954 - 3.0850 1.00 2654 118 0.1949 0.2506 REMARK 3 5 3.0850 - 2.8639 1.00 2656 125 0.2074 0.2812 REMARK 3 6 2.8639 - 2.6951 1.00 2633 118 0.2002 0.2956 REMARK 3 7 2.6951 - 2.5601 1.00 2605 159 0.2125 0.2775 REMARK 3 8 2.5601 - 2.4487 1.00 2598 153 0.2201 0.2825 REMARK 3 9 2.4487 - 2.3544 0.98 2547 146 0.2188 0.3234 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.900 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 : 0.008 4244 REMARK 3 ANGLE : 1.009 5790 REMARK 3 CHIRALITY : 0.056 614 REMARK 3 PLANARITY : 0.006 741 REMARK 3 DIHEDRAL : 20.767 2488 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -25.2804 9.4402 -34.7879 REMARK 3 T TENSOR REMARK 3 T11: 0.1838 T22: 0.2053 REMARK 3 T33: 0.1937 T12: 0.0360 REMARK 3 T13: -0.0535 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 0.8755 L22: 1.0836 REMARK 3 L33: 0.9349 L12: -0.0646 REMARK 3 L13: -0.2630 L23: 0.0208 REMARK 3 S TENSOR REMARK 3 S11: -0.1097 S12: 0.0086 S13: 0.0979 REMARK 3 S21: -0.0402 S22: 0.0889 S23: -0.0114 REMARK 3 S31: -0.0359 S32: -0.0539 S33: 0.0333 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 5ISY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-15 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25141 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : 25.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : 0.12000 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 REMARK 200 STARTING MODEL: 2GB5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM MALONATE, BIS-TRIS, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 26.20550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.86950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.35100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.86950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.20550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.35100 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: 5410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 ALA A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 253 REMARK 465 ALA A 254 REMARK 465 GLU A 257 REMARK 465 ALA C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 LEU C 8 REMARK 465 CYS C 252 REMARK 465 ARG C 253 REMARK 465 ALA C 254 REMARK 465 GLU C 255 REMARK 465 TYR C 256 REMARK 465 GLU C 257 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 A 7 CG CD CE NZ REMARK 470 CYS A 116 SG REMARK 470 CYS A 119 SG REMARK 470 ARG A 120 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 149 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 181 CD1 REMARK 470 ARG C 62 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 69 CZ NH1 NH2 REMARK 470 HIS C 149 CE1 NE2 REMARK 470 ILE C 181 CD1 REMARK 470 LYS C 182 CD CE NZ REMARK 470 LYS C 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 OD2 ASP A 64 O HOH A 401 1.97 REMARK 500 O HOH C 453 O HOH C 499 2.09 REMARK 500 O ASP A 230 O HOH A 402 2.11 REMARK 500 N LEU C 186 O HOH C 401 2.15 REMARK 500 O CYS A 252 N GLU A 255 2.17 REMARK 500 O HOH C 492 O HOH C 493 2.18 REMARK 500 O HOH A 410 O HOH C 469 2.19 REMARK 500 O ARG C 42 O HOH C 402 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 101 CB CYS A 101 SG -0.140 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 CYS A 101 CA - CB - SG ANGL. DEV. = 7.1 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 ASP A 138 -102.90 60.46 REMARK 500 HIS A 149 -66.23 -93.47 REMARK 500 ARG A 150 83.11 63.08 REMARK 500 ASN A 151 3.54 -158.75 REMARK 500 GLN A 198 47.87 -161.91 REMARK 500 LYS C 25 13.51 59.41 REMARK 500 ASP C 138 -119.65 49.43 REMARK 500 ARG C 150 72.19 52.98 REMARK 500 ASN C 151 22.60 -140.46 REMARK 500 GLN C 198 43.12 -155.90 REMARK 500 ASP C 209 -67.27 -92.58 REMARK 500 ASP C 230 56.21 -157.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 100 CYS A 101 -149.42 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 98 SG REMARK 620 2 CYS A 101 SG 125.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 98 SG REMARK 620 2 CYS C 101 SG 109.1 REMARK 620 3 CYS C 116 SG 110.2 100.4 REMARK 620 4 CYS C 119 SG 105.4 117.2 114.5 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD C 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IS3 RELATED DB: PDB DBREF 5ISY A 1 257 UNP P32664 NUDC_ECOLI 1 257 DBREF 5ISY C 1 257 UNP P32664 NUDC_ECOLI 1 257 SEQADV 5ISY ALA A -1 UNP P32664 EXPRESSION TAG SEQADV 5ISY HIS A 0 UNP P32664 EXPRESSION TAG SEQADV 5ISY GLN A 178 UNP P32664 GLU 178 ENGINEERED MUTATION SEQADV 5ISY ALA C -1 UNP P32664 EXPRESSION TAG SEQADV 5ISY HIS C 0 UNP P32664 EXPRESSION TAG SEQADV 5ISY GLN C 178 UNP P32664 GLU 178 ENGINEERED MUTATION SEQRES 1 A 259 ALA HIS MET ASP ARG ILE ILE GLU LYS LEU ASP HIS GLY SEQRES 2 A 259 TRP TRP VAL VAL SER HIS GLU GLN LYS LEU TRP LEU PRO SEQRES 3 A 259 LYS GLY GLU LEU PRO TYR GLY GLU ALA ALA ASN PHE ASP SEQRES 4 A 259 LEU VAL GLY GLN ARG ALA LEU GLN ILE GLY GLU TRP GLN SEQRES 5 A 259 GLY GLU PRO VAL TRP LEU VAL GLN GLN GLN ARG ARG HIS SEQRES 6 A 259 ASP MET GLY SER VAL ARG GLN VAL ILE ASP LEU ASP VAL SEQRES 7 A 259 GLY LEU PHE GLN LEU ALA GLY ARG GLY VAL GLN LEU ALA SEQRES 8 A 259 GLU PHE TYR ARG SER HIS LYS TYR CYS GLY TYR CYS GLY SEQRES 9 A 259 HIS GLU MET TYR PRO SER LYS THR GLU TRP ALA MET LEU SEQRES 10 A 259 CYS SER HIS CYS ARG GLU ARG TYR TYR PRO GLN ILE ALA SEQRES 11 A 259 PRO CYS ILE ILE VAL ALA ILE ARG ARG ASP ASP SER ILE SEQRES 12 A 259 LEU LEU ALA GLN HIS THR ARG HIS ARG ASN GLY VAL HIS SEQRES 13 A 259 THR VAL LEU ALA GLY PHE VAL GLU VAL GLY GLU THR LEU SEQRES 14 A 259 GLU GLN ALA VAL ALA ARG GLU VAL MET GLU GLN SER GLY SEQRES 15 A 259 ILE LYS VAL LYS ASN LEU ARG TYR VAL THR SER GLN PRO SEQRES 16 A 259 TRP PRO PHE PRO GLN SER LEU MET THR ALA PHE MET ALA SEQRES 17 A 259 GLU TYR ASP SER GLY ASP ILE VAL ILE ASP PRO LYS GLU SEQRES 18 A 259 LEU LEU GLU ALA ASN TRP TYR ARG TYR ASP ASP LEU PRO SEQRES 19 A 259 LEU LEU PRO PRO PRO GLY THR VAL ALA ARG ARG LEU ILE SEQRES 20 A 259 GLU ASP THR VAL ALA MET CYS ARG ALA GLU TYR GLU SEQRES 1 C 259 ALA HIS MET ASP ARG ILE ILE GLU LYS LEU ASP HIS GLY SEQRES 2 C 259 TRP TRP VAL VAL SER HIS GLU GLN LYS LEU TRP LEU PRO SEQRES 3 C 259 LYS GLY GLU LEU PRO TYR GLY GLU ALA ALA ASN PHE ASP SEQRES 4 C 259 LEU VAL GLY GLN ARG ALA LEU GLN ILE GLY GLU TRP GLN SEQRES 5 C 259 GLY GLU PRO VAL TRP LEU VAL GLN GLN GLN ARG ARG HIS SEQRES 6 C 259 ASP MET GLY SER VAL ARG GLN VAL ILE ASP LEU ASP VAL SEQRES 7 C 259 GLY LEU PHE GLN LEU ALA GLY ARG GLY VAL GLN LEU ALA SEQRES 8 C 259 GLU PHE TYR ARG SER HIS LYS TYR CYS GLY TYR CYS GLY SEQRES 9 C 259 HIS GLU MET TYR PRO SER LYS THR GLU TRP ALA MET LEU SEQRES 10 C 259 CYS SER HIS CYS ARG GLU ARG TYR TYR PRO GLN ILE ALA SEQRES 11 C 259 PRO CYS ILE ILE VAL ALA ILE ARG ARG ASP ASP SER ILE SEQRES 12 C 259 LEU LEU ALA GLN HIS THR ARG HIS ARG ASN GLY VAL HIS SEQRES 13 C 259 THR VAL LEU ALA GLY PHE VAL GLU VAL GLY GLU THR LEU SEQRES 14 C 259 GLU GLN ALA VAL ALA ARG GLU VAL MET GLU GLN SER GLY SEQRES 15 C 259 ILE LYS VAL LYS ASN LEU ARG TYR VAL THR SER GLN PRO SEQRES 16 C 259 TRP PRO PHE PRO GLN SER LEU MET THR ALA PHE MET ALA SEQRES 17 C 259 GLU TYR ASP SER GLY ASP ILE VAL ILE ASP PRO LYS GLU SEQRES 18 C 259 LEU LEU GLU ALA ASN TRP TYR ARG TYR ASP ASP LEU PRO SEQRES 19 C 259 LEU LEU PRO PRO PRO GLY THR VAL ALA ARG ARG LEU ILE SEQRES 20 C 259 GLU ASP THR VAL ALA MET CYS ARG ALA GLU TYR GLU HET ZN A 301 1 HET NAD A 302 44 HET ZN C 301 1 HET NAD C 302 44 HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 7 HOH *208(H2 O) HELIX 1 AA1 PRO A 24 GLU A 27 5 4 HELIX 2 AA2 ALA A 34 ASP A 37 5 4 HELIX 3 AA3 SER A 67 ILE A 72 5 6 HELIX 4 AA4 ASP A 75 SER A 94 1 20 HELIX 5 AA5 THR A 166 GLY A 180 1 15 HELIX 6 AA6 THR A 239 CYS A 252 1 14 HELIX 7 AA7 PRO C 24 GLU C 27 5 4 HELIX 8 AA8 ALA C 34 ASP C 37 5 4 HELIX 9 AA9 SER C 67 ILE C 72 5 6 HELIX 10 AB1 ASP C 75 SER C 94 1 20 HELIX 11 AB2 THR C 166 GLY C 180 1 15 HELIX 12 AB3 THR C 239 ALA C 250 1 12 SHEET 1 AA1 5 ARG A 3 ILE A 4 0 SHEET 2 AA1 5 ARG A 42 TRP A 49 -1 O ALA A 43 N ARG A 3 SHEET 3 AA1 5 GLU A 52 GLN A 58 -1 O GLU A 52 N TRP A 49 SHEET 4 AA1 5 HIS A 10 HIS A 17 1 N VAL A 14 O TRP A 55 SHEET 5 AA1 5 TYR A 30 GLU A 32 -1 O GLY A 31 N GLY A 11 SHEET 1 AA2 6 ARG A 3 ILE A 4 0 SHEET 2 AA2 6 ARG A 42 TRP A 49 -1 O ALA A 43 N ARG A 3 SHEET 3 AA2 6 GLU A 52 GLN A 58 -1 O GLU A 52 N TRP A 49 SHEET 4 AA2 6 HIS A 10 HIS A 17 1 N VAL A 14 O TRP A 55 SHEET 5 AA2 6 LYS A 20 TRP A 22 -1 O TRP A 22 N VAL A 15 SHEET 6 AA2 6 MET A 65 GLY A 66 -1 O GLY A 66 N LEU A 21 SHEET 1 AA3 3 MET A 105 PRO A 107 0 SHEET 2 AA3 3 MET A 114 CYS A 116 -1 O LEU A 115 N TYR A 106 SHEET 3 AA3 3 ARG A 122 TYR A 123 -1 O TYR A 123 N MET A 114 SHEET 1 AA4 4 LEU A 157 PHE A 160 0 SHEET 2 AA4 4 ALA A 128 ARG A 137 -1 N ILE A 131 O GLY A 159 SHEET 3 AA4 4 SER A 199 SER A 210 1 O TYR A 208 N ARG A 136 SHEET 4 AA4 4 LYS A 182 TRP A 194 -1 N LYS A 184 O GLU A 207 SHEET 1 AA5 4 LEU A 157 PHE A 160 0 SHEET 2 AA5 4 ALA A 128 ARG A 137 -1 N ILE A 131 O GLY A 159 SHEET 3 AA5 4 SER A 140 HIS A 146 -1 O SER A 140 N ARG A 137 SHEET 4 AA5 4 LEU A 220 ARG A 227 -1 O ASN A 224 N LEU A 143 SHEET 1 AA6 5 ARG C 3 ILE C 4 0 SHEET 2 AA6 5 ARG C 42 TRP C 49 -1 O ALA C 43 N ARG C 3 SHEET 3 AA6 5 GLU C 52 GLN C 58 -1 O GLU C 52 N TRP C 49 SHEET 4 AA6 5 HIS C 10 HIS C 17 1 N VAL C 14 O TRP C 55 SHEET 5 AA6 5 TYR C 30 GLU C 32 -1 O GLY C 31 N GLY C 11 SHEET 1 AA7 6 ARG C 3 ILE C 4 0 SHEET 2 AA7 6 ARG C 42 TRP C 49 -1 O ALA C 43 N ARG C 3 SHEET 3 AA7 6 GLU C 52 GLN C 58 -1 O GLU C 52 N TRP C 49 SHEET 4 AA7 6 HIS C 10 HIS C 17 1 N VAL C 14 O TRP C 55 SHEET 5 AA7 6 LYS C 20 TRP C 22 -1 O TRP C 22 N VAL C 15 SHEET 6 AA7 6 MET C 65 GLY C 66 -1 O GLY C 66 N LEU C 21 SHEET 1 AA8 3 TYR C 106 PRO C 107 0 SHEET 2 AA8 3 MET C 114 LEU C 115 -1 O LEU C 115 N TYR C 106 SHEET 3 AA8 3 ARG C 122 TYR C 123 -1 O TYR C 123 N MET C 114 SHEET 1 AA9 5 HIS C 154 THR C 155 0 SHEET 2 AA9 5 SER C 140 HIS C 146 -1 N ALA C 144 O THR C 155 SHEET 3 AA9 5 ALA C 128 ARG C 137 -1 N ARG C 137 O SER C 140 SHEET 4 AA9 5 SER C 199 SER C 210 1 O THR C 202 N CYS C 130 SHEET 5 AA9 5 LYS C 182 TRP C 194 -1 N ARG C 187 O MET C 205 SHEET 1 AB1 4 LEU C 157 PHE C 160 0 SHEET 2 AB1 4 ALA C 128 ARG C 137 -1 N ILE C 131 O GLY C 159 SHEET 3 AB1 4 SER C 140 HIS C 146 -1 O SER C 140 N ARG C 137 SHEET 4 AB1 4 LEU C 220 ARG C 227 -1 O LEU C 221 N GLN C 145 LINK SG CYS A 98 ZN ZN A 301 1555 1555 2.30 LINK SG CYS A 101 ZN ZN A 301 1555 1555 2.53 LINK SG CYS C 98 ZN ZN C 301 1555 1555 2.38 LINK SG CYS C 101 ZN ZN C 301 1555 1555 2.34 LINK SG CYS C 116 ZN ZN C 301 1555 1555 2.29 LINK SG CYS C 119 ZN ZN C 301 1555 1555 2.21 CISPEP 1 PHE A 196 PRO A 197 0 2.99 CISPEP 2 PHE C 196 PRO C 197 0 -2.74 SITE 1 AC1 4 CYS A 98 CYS A 101 CYS A 116 CYS A 119 SITE 1 AC2 15 CYS A 130 ILE A 132 PHE A 160 GLN A 192 SITE 2 AC2 15 TRP A 194 PHE A 196 SER A 199 MET A 201 SITE 3 AC2 15 THR A 239 VAL A 240 ALA A 241 HOH A 413 SITE 4 AC2 15 HOH A 474 GLU C 111 TYR C 124 SITE 1 AC3 4 CYS C 98 CYS C 101 CYS C 116 CYS C 119 SITE 1 AC4 12 GLU A 111 TYR A 124 ALA C 128 CYS C 130 SITE 2 AC4 12 PHE C 160 TRP C 194 PHE C 196 SER C 199 SITE 3 AC4 12 MET C 201 VAL C 240 ALA C 241 HOH C 470 CRYST1 52.411 98.702 113.739 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 0.019080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008792 0.00000