HEADER OXIDOREDUCTASE 26-OCT-11 3UCE TITLE CRYSTAL STRUCTURE OF A SMALL-CHAIN DEHYDROGENASE IN COMPLEX WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHYDROGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 196600; SOURCE 4 STRAIN: YJ016; SOURCE 5 GENE: VVA1599; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PACYCDUET-I KEYWDS ROSSMANN FOLD, SMALL-CHAIN DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.BUYSSCHAERT,K.VERSTRAETE,S.SAVVIDES,B.VERGAUWEN REVDAT 2 13-MAR-13 3UCE 1 JRNL REVDAT 1 28-NOV-12 3UCE 0 JRNL AUTH G.BUYSSCHAERT,K.VERSTRAETE,S.N.SAVVIDES,B.VERGAUWEN JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF AN ATYPICAL JRNL TITL 2 SHORT-CHAIN DEHYDROGENASE/REDUCTASE REVEALS AN UNUSUAL JRNL TITL 3 COFACTOR PREFERENCE. JRNL REF FEBS J. V. 280 1358 2013 JRNL REFN ISSN 1742-464X JRNL PMID 23311896 JRNL DOI 10.1111/FEBS.12128 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 84914 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4243 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 39.2098 - 5.5819 0.99 2766 144 0.1900 0.1990 REMARK 3 2 5.5819 - 4.4325 0.99 2724 145 0.1495 0.1688 REMARK 3 3 4.4325 - 3.8727 0.99 2713 140 0.1458 0.1613 REMARK 3 4 3.8727 - 3.5189 0.98 2664 141 0.1627 0.1966 REMARK 3 5 3.5189 - 3.2668 0.99 2681 140 0.1681 0.2151 REMARK 3 6 3.2668 - 3.0743 0.99 2721 143 0.1731 0.2037 REMARK 3 7 3.0743 - 2.9204 1.00 2702 141 0.1648 0.2156 REMARK 3 8 2.9204 - 2.7933 0.99 2702 142 0.1619 0.2308 REMARK 3 9 2.7933 - 2.6858 1.00 2698 144 0.1586 0.2072 REMARK 3 10 2.6858 - 2.5931 1.00 2725 145 0.1597 0.2026 REMARK 3 11 2.5931 - 2.5121 1.00 2713 140 0.1658 0.2311 REMARK 3 12 2.5121 - 2.4403 1.00 2697 145 0.1632 0.2190 REMARK 3 13 2.4403 - 2.3760 1.00 2669 138 0.1684 0.2151 REMARK 3 14 2.3760 - 2.3181 0.99 2677 142 0.1685 0.2665 REMARK 3 15 2.3181 - 2.2654 1.00 2726 147 0.1628 0.2304 REMARK 3 16 2.2654 - 2.2172 1.00 2713 143 0.1716 0.2109 REMARK 3 17 2.2172 - 2.1728 1.00 2660 141 0.1743 0.2464 REMARK 3 18 2.1728 - 2.1318 1.00 2719 139 0.1792 0.2073 REMARK 3 19 2.1318 - 2.0938 1.00 2682 146 0.1885 0.2792 REMARK 3 20 2.0938 - 2.0583 1.00 2705 137 0.1985 0.2406 REMARK 3 21 2.0583 - 2.0251 1.00 2728 138 0.1917 0.2762 REMARK 3 22 2.0251 - 1.9939 1.00 2641 142 0.1961 0.2300 REMARK 3 23 1.9939 - 1.9646 1.00 2745 147 0.1943 0.2800 REMARK 3 24 1.9646 - 1.9369 1.00 2670 147 0.2115 0.2389 REMARK 3 25 1.9369 - 1.9107 1.00 2695 140 0.2175 0.2320 REMARK 3 26 1.9107 - 1.8859 1.00 2670 131 0.2340 0.3074 REMARK 3 27 1.8859 - 1.8624 1.00 2740 141 0.2455 0.3158 REMARK 3 28 1.8624 - 1.8399 1.00 2686 142 0.2580 0.3111 REMARK 3 29 1.8399 - 1.8185 1.00 2707 147 0.2546 0.2977 REMARK 3 30 1.8185 - 1.7981 0.87 2332 125 0.2725 0.3042 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.77 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 45.28 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.80600 REMARK 3 B22 (A**2) : 0.98440 REMARK 3 B33 (A**2) : 6.82160 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.87500 REMARK 3 B23 (A**2) : -0.00000 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 6746 REMARK 3 ANGLE : 1.096 9204 REMARK 3 CHIRALITY : 0.059 1104 REMARK 3 PLANARITY : 0.004 1135 REMARK 3 DIHEDRAL : 14.443 2334 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 3UCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-11. REMARK 100 THE RCSB ID CODE IS RCSB068577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99993 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.798 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.38 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.410 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: PDB ENTRY 1O5I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 18% PEG-5000, REMARK 280 PROTEIN CONCENTRATION: 8 MG/ML, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 48.13000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 MET A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 MET B 1 REMARK 465 MET B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 MET C 1 REMARK 465 MET C 2 REMARK 465 GLY C 3 REMARK 465 SER C 4 REMARK 465 MET D 1 REMARK 465 MET D 2 REMARK 465 GLY D 3 REMARK 465 SER D 4 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 ASP A 5 CG OD1 OD2 REMARK 470 LYS A 24 NZ REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 HIS A 30 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 ASN A 170 CG OD1 ND2 REMARK 470 ASP A 172 CG OD1 OD2 REMARK 470 ARG A 180 CD NE CZ NH1 NH2 REMARK 470 ASP B 5 CG OD1 OD2 REMARK 470 LYS B 24 CE NZ REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 ASN B 170 CG OD1 ND2 REMARK 470 ASP B 172 CG OD1 OD2 REMARK 470 ASP B 173 CG OD1 OD2 REMARK 470 GLN B 179 CG CD OE1 NE2 REMARK 470 ARG B 180 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 205 CG CD OE1 NE2 REMARK 470 ASP C 5 CG OD1 OD2 REMARK 470 LYS C 24 CD CE NZ REMARK 470 GLU C 29 CG CD OE1 OE2 REMARK 470 LYS C 48 CD CE NZ REMARK 470 GLU C 80 CG CD OE1 OE2 REMARK 470 LYS C 130 CE NZ REMARK 470 LYS C 167 CG CD CE NZ REMARK 470 ARG C 180 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 205 CG CD OE1 NE2 REMARK 470 ASP D 5 CG OD1 OD2 REMARK 470 LYS D 24 CE NZ REMARK 470 LYS D 48 CD CE NZ REMARK 470 LYS D 167 CE NZ REMARK 470 ARG D 180 CG CD NE CZ NH1 NH2 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 HG1 THR D 15 HG SER D 37 1.33 REMARK 500 HG1 THR C 15 HG SER C 37 1.34 REMARK 500 OE1 GLU D 80 O HOH D 983 2.02 REMARK 500 O HOH C 300 O HOH D 608 2.06 REMARK 500 O MET D 169 O HOH D 873 2.06 REMARK 500 O HOH D 770 O HOH D 865 2.10 REMARK 500 O HOH B 290 O HOH D 288 2.11 REMARK 500 O HOH B 766 O HOH B 769 2.11 REMARK 500 O HOH C 742 O HOH C 849 2.13 REMARK 500 O HOH B 832 O HOH B 857 2.14 REMARK 500 O HOH B 465 O HOH B 561 2.14 REMARK 500 O HOH C 848 O HOH C 874 2.14 REMARK 500 OD1 ASP C 46 O HOH C 742 2.15 REMARK 500 O HOH B 494 O HOH B 552 2.16 REMARK 500 O HOH D 613 O HOH D 878 2.16 REMARK 500 O HOH A 280 O HOH D 919 2.17 REMARK 500 O HOH B 735 O HOH B 887 2.17 REMARK 500 O HOH B 403 O HOH B 494 2.18 REMARK 500 O HOH C 830 O HOH C 956 2.18 REMARK 500 O HOH B 696 O HOH B 731 2.19 REMARK 500 O SER D 69 O HOH D 798 2.19 REMARK 500 O HOH C 643 O HOH C 670 2.19 REMARK 500 O HOH A 497 O HOH D 376 2.19 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 O HOH C 877 O HOH C 980 2556 2.15 REMARK 500 O HOH A 947 O HOH B 907 1455 2.18 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 SER A 37 -166.33 -171.00 REMARK 500 SER A 116 -106.16 -108.95 REMARK 500 ASN A 126 13.91 81.01 REMARK 500 SER B 37 -169.40 -162.11 REMARK 500 SER B 116 -107.12 -111.40 REMARK 500 ALA B 171 -12.72 -46.20 REMARK 500 SER C 37 -177.13 -176.00 REMARK 500 SER C 116 -111.97 -111.95 REMARK 500 SER D 116 -110.18 -113.77 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 863 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH C 672 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH C 846 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH C 848 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH D 784 DISTANCE = 5.41 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP C 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP D 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UCF RELATED DB: PDB DBREF 3UCE A 1 223 UNP Q7MBY8 Q7MBY8_VIBVY 1 223 DBREF 3UCE B 1 223 UNP Q7MBY8 Q7MBY8_VIBVY 1 223 DBREF 3UCE C 1 223 UNP Q7MBY8 Q7MBY8_VIBVY 1 223 DBREF 3UCE D 1 223 UNP Q7MBY8 Q7MBY8_VIBVY 1 223 SEQRES 1 A 223 MET MET GLY SER ASP LYS THR VAL TYR VAL VAL LEU GLY SEQRES 2 A 223 GLY THR SER GLY ILE GLY ALA GLU LEU ALA LYS GLN LEU SEQRES 3 A 223 GLU SER GLU HIS THR ILE VAL HIS VAL ALA SER ARG GLN SEQRES 4 A 223 THR GLY LEU ASP ILE SER ASP GLU LYS SER VAL TYR HIS SEQRES 5 A 223 TYR PHE GLU THR ILE GLY ALA PHE ASP HIS LEU ILE VAL SEQRES 6 A 223 THR ALA GLY SER TYR ALA PRO ALA GLY LYS VAL VAL ASP SEQRES 7 A 223 VAL GLU VAL THR GLN ALA LYS TYR ALA PHE ASP THR LYS SEQRES 8 A 223 PHE TRP GLY ALA VAL LEU ALA ALA LYS HIS GLY ALA ARG SEQRES 9 A 223 TYR LEU LYS GLN GLY GLY SER ILE THR LEU THR SER GLY SEQRES 10 A 223 MET LEU SER ARG LYS VAL VAL ALA ASN THR TYR VAL LYS SEQRES 11 A 223 ALA ALA ILE ASN ALA ALA ILE GLU ALA THR THR LYS VAL SEQRES 12 A 223 LEU ALA LYS GLU LEU ALA PRO ILE ARG VAL ASN ALA ILE SEQRES 13 A 223 SER PRO GLY LEU THR LYS THR GLU ALA TYR LYS GLY MET SEQRES 14 A 223 ASN ALA ASP ASP ARG ASP ALA MET TYR GLN ARG THR GLN SEQRES 15 A 223 SER HIS LEU PRO VAL GLY LYS VAL GLY GLU ALA SER ASP SEQRES 16 A 223 ILE ALA MET ALA TYR LEU PHE ALA ILE GLN ASN SER TYR SEQRES 17 A 223 MET THR GLY THR VAL ILE ASP VAL ASP GLY GLY ALA LEU SEQRES 18 A 223 LEU GLY SEQRES 1 B 223 MET MET GLY SER ASP LYS THR VAL TYR VAL VAL LEU GLY SEQRES 2 B 223 GLY THR SER GLY ILE GLY ALA GLU LEU ALA LYS GLN LEU SEQRES 3 B 223 GLU SER GLU HIS THR ILE VAL HIS VAL ALA SER ARG GLN SEQRES 4 B 223 THR GLY LEU ASP ILE SER ASP GLU LYS SER VAL TYR HIS SEQRES 5 B 223 TYR PHE GLU THR ILE GLY ALA PHE ASP HIS LEU ILE VAL SEQRES 6 B 223 THR ALA GLY SER TYR ALA PRO ALA GLY LYS VAL VAL ASP SEQRES 7 B 223 VAL GLU VAL THR GLN ALA LYS TYR ALA PHE ASP THR LYS SEQRES 8 B 223 PHE TRP GLY ALA VAL LEU ALA ALA LYS HIS GLY ALA ARG SEQRES 9 B 223 TYR LEU LYS GLN GLY GLY SER ILE THR LEU THR SER GLY SEQRES 10 B 223 MET LEU SER ARG LYS VAL VAL ALA ASN THR TYR VAL LYS SEQRES 11 B 223 ALA ALA ILE ASN ALA ALA ILE GLU ALA THR THR LYS VAL SEQRES 12 B 223 LEU ALA LYS GLU LEU ALA PRO ILE ARG VAL ASN ALA ILE SEQRES 13 B 223 SER PRO GLY LEU THR LYS THR GLU ALA TYR LYS GLY MET SEQRES 14 B 223 ASN ALA ASP ASP ARG ASP ALA MET TYR GLN ARG THR GLN SEQRES 15 B 223 SER HIS LEU PRO VAL GLY LYS VAL GLY GLU ALA SER ASP SEQRES 16 B 223 ILE ALA MET ALA TYR LEU PHE ALA ILE GLN ASN SER TYR SEQRES 17 B 223 MET THR GLY THR VAL ILE ASP VAL ASP GLY GLY ALA LEU SEQRES 18 B 223 LEU GLY SEQRES 1 C 223 MET MET GLY SER ASP LYS THR VAL TYR VAL VAL LEU GLY SEQRES 2 C 223 GLY THR SER GLY ILE GLY ALA GLU LEU ALA LYS GLN LEU SEQRES 3 C 223 GLU SER GLU HIS THR ILE VAL HIS VAL ALA SER ARG GLN SEQRES 4 C 223 THR GLY LEU ASP ILE SER ASP GLU LYS SER VAL TYR HIS SEQRES 5 C 223 TYR PHE GLU THR ILE GLY ALA PHE ASP HIS LEU ILE VAL SEQRES 6 C 223 THR ALA GLY SER TYR ALA PRO ALA GLY LYS VAL VAL ASP SEQRES 7 C 223 VAL GLU VAL THR GLN ALA LYS TYR ALA PHE ASP THR LYS SEQRES 8 C 223 PHE TRP GLY ALA VAL LEU ALA ALA LYS HIS GLY ALA ARG SEQRES 9 C 223 TYR LEU LYS GLN GLY GLY SER ILE THR LEU THR SER GLY SEQRES 10 C 223 MET LEU SER ARG LYS VAL VAL ALA ASN THR TYR VAL LYS SEQRES 11 C 223 ALA ALA ILE ASN ALA ALA ILE GLU ALA THR THR LYS VAL SEQRES 12 C 223 LEU ALA LYS GLU LEU ALA PRO ILE ARG VAL ASN ALA ILE SEQRES 13 C 223 SER PRO GLY LEU THR LYS THR GLU ALA TYR LYS GLY MET SEQRES 14 C 223 ASN ALA ASP ASP ARG ASP ALA MET TYR GLN ARG THR GLN SEQRES 15 C 223 SER HIS LEU PRO VAL GLY LYS VAL GLY GLU ALA SER ASP SEQRES 16 C 223 ILE ALA MET ALA TYR LEU PHE ALA ILE GLN ASN SER TYR SEQRES 17 C 223 MET THR GLY THR VAL ILE ASP VAL ASP GLY GLY ALA LEU SEQRES 18 C 223 LEU GLY SEQRES 1 D 223 MET MET GLY SER ASP LYS THR VAL TYR VAL VAL LEU GLY SEQRES 2 D 223 GLY THR SER GLY ILE GLY ALA GLU LEU ALA LYS GLN LEU SEQRES 3 D 223 GLU SER GLU HIS THR ILE VAL HIS VAL ALA SER ARG GLN SEQRES 4 D 223 THR GLY LEU ASP ILE SER ASP GLU LYS SER VAL TYR HIS SEQRES 5 D 223 TYR PHE GLU THR ILE GLY ALA PHE ASP HIS LEU ILE VAL SEQRES 6 D 223 THR ALA GLY SER TYR ALA PRO ALA GLY LYS VAL VAL ASP SEQRES 7 D 223 VAL GLU VAL THR GLN ALA LYS TYR ALA PHE ASP THR LYS SEQRES 8 D 223 PHE TRP GLY ALA VAL LEU ALA ALA LYS HIS GLY ALA ARG SEQRES 9 D 223 TYR LEU LYS GLN GLY GLY SER ILE THR LEU THR SER GLY SEQRES 10 D 223 MET LEU SER ARG LYS VAL VAL ALA ASN THR TYR VAL LYS SEQRES 11 D 223 ALA ALA ILE ASN ALA ALA ILE GLU ALA THR THR LYS VAL SEQRES 12 D 223 LEU ALA LYS GLU LEU ALA PRO ILE ARG VAL ASN ALA ILE SEQRES 13 D 223 SER PRO GLY LEU THR LYS THR GLU ALA TYR LYS GLY MET SEQRES 14 D 223 ASN ALA ASP ASP ARG ASP ALA MET TYR GLN ARG THR GLN SEQRES 15 D 223 SER HIS LEU PRO VAL GLY LYS VAL GLY GLU ALA SER ASP SEQRES 16 D 223 ILE ALA MET ALA TYR LEU PHE ALA ILE GLN ASN SER TYR SEQRES 17 D 223 MET THR GLY THR VAL ILE ASP VAL ASP GLY GLY ALA LEU SEQRES 18 D 223 LEU GLY HET NDP A 500 74 HET NDP B 500 74 HET NDP C 500 74 HET NDP D 500 74 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 5 NDP 4(C21 H30 N7 O17 P3) FORMUL 9 HOH *989(H2 O) HELIX 1 1 SER A 16 GLU A 27 1 12 HELIX 2 2 SER A 37 GLY A 41 5 5 HELIX 3 3 ASP A 46 GLY A 58 1 13 HELIX 4 4 GLU A 80 ALA A 103 1 24 HELIX 5 5 GLY A 117 ARG A 121 5 5 HELIX 6 6 THR A 127 ALA A 149 1 23 HELIX 7 7 THR A 163 LYS A 167 5 5 HELIX 8 8 ASN A 170 LEU A 185 1 16 HELIX 9 9 GLU A 192 ASN A 206 1 15 HELIX 10 10 GLY A 219 GLY A 223 5 5 HELIX 11 11 SER B 16 GLU B 27 1 12 HELIX 12 12 SER B 37 GLY B 41 5 5 HELIX 13 13 ASP B 46 GLY B 58 1 13 HELIX 14 14 GLU B 80 ALA B 103 1 24 HELIX 15 15 GLY B 117 ARG B 121 5 5 HELIX 16 16 THR B 127 ALA B 149 1 23 HELIX 17 17 THR B 163 LYS B 167 5 5 HELIX 18 18 ASN B 170 LEU B 185 1 16 HELIX 19 19 GLU B 192 ASN B 206 1 15 HELIX 20 20 GLY B 219 GLY B 223 5 5 HELIX 21 21 SER C 16 GLU C 27 1 12 HELIX 22 22 SER C 37 GLY C 41 5 5 HELIX 23 23 ASP C 46 GLY C 58 1 13 HELIX 24 24 GLU C 80 ALA C 103 1 24 HELIX 25 25 GLY C 117 ARG C 121 5 5 HELIX 26 26 THR C 127 ALA C 149 1 23 HELIX 27 27 THR C 163 LYS C 167 5 5 HELIX 28 28 ASN C 170 LEU C 185 1 16 HELIX 29 29 ALA C 193 ASN C 206 1 14 HELIX 30 30 GLY C 219 GLY C 223 5 5 HELIX 31 31 SER D 16 GLU D 27 1 12 HELIX 32 32 SER D 37 GLY D 41 5 5 HELIX 33 33 ASP D 46 GLY D 58 1 13 HELIX 34 34 GLU D 80 ALA D 103 1 24 HELIX 35 35 GLY D 117 ARG D 121 5 5 HELIX 36 36 THR D 127 ALA D 149 1 23 HELIX 37 37 THR D 163 LYS D 167 5 5 HELIX 38 38 ASN D 170 LEU D 185 1 16 HELIX 39 39 GLU D 192 ASN D 206 1 15 HELIX 40 40 GLY D 219 GLY D 223 5 5 SHEET 1 A 6 THR A 31 ALA A 36 0 SHEET 2 A 6 THR A 7 LEU A 12 1 N VAL A 11 O HIS A 34 SHEET 3 A 6 PHE A 60 VAL A 65 1 O ILE A 64 N VAL A 10 SHEET 4 A 6 LEU A 106 THR A 115 1 O THR A 113 N LEU A 63 SHEET 5 A 6 ARG A 152 PRO A 158 1 O ASN A 154 N LEU A 114 SHEET 6 A 6 VAL A 213 VAL A 216 1 O ILE A 214 N SER A 157 SHEET 1 B 6 THR B 31 ALA B 36 0 SHEET 2 B 6 THR B 7 LEU B 12 1 N VAL B 11 O HIS B 34 SHEET 3 B 6 PHE B 60 VAL B 65 1 O ILE B 64 N VAL B 10 SHEET 4 B 6 LEU B 106 THR B 115 1 O THR B 113 N LEU B 63 SHEET 5 B 6 ARG B 152 PRO B 158 1 O ARG B 152 N ILE B 112 SHEET 6 B 6 VAL B 213 VAL B 216 1 O ILE B 214 N SER B 157 SHEET 1 C 6 THR C 31 ALA C 36 0 SHEET 2 C 6 THR C 7 LEU C 12 1 N TYR C 9 O ILE C 32 SHEET 3 C 6 PHE C 60 VAL C 65 1 O ILE C 64 N VAL C 10 SHEET 4 C 6 LEU C 106 THR C 115 1 O THR C 113 N LEU C 63 SHEET 5 C 6 ARG C 152 PRO C 158 1 O ARG C 152 N ILE C 112 SHEET 6 C 6 VAL C 213 VAL C 216 1 O ILE C 214 N SER C 157 SHEET 1 D 2 THR C 161 LYS C 162 0 SHEET 2 D 2 GLY C 191 GLU C 192 1 O GLY C 191 N LYS C 162 SHEET 1 E 6 THR D 31 ALA D 36 0 SHEET 2 E 6 THR D 7 LEU D 12 1 N TYR D 9 O HIS D 34 SHEET 3 E 6 PHE D 60 VAL D 65 1 O ILE D 64 N VAL D 10 SHEET 4 E 6 LEU D 106 THR D 115 1 O LYS D 107 N PHE D 60 SHEET 5 E 6 ARG D 152 PRO D 158 1 O ARG D 152 N ILE D 112 SHEET 6 E 6 VAL D 213 VAL D 216 1 O ILE D 214 N SER D 157 CISPEP 1 ALA A 149 PRO A 150 0 11.74 CISPEP 2 ALA B 149 PRO B 150 0 7.94 CISPEP 3 ALA C 149 PRO C 150 0 12.21 CISPEP 4 ALA D 149 PRO D 150 0 7.42 SITE 1 AC1 32 GLY A 13 THR A 15 SER A 16 GLY A 17 SITE 2 AC1 32 ILE A 18 SER A 37 ARG A 38 GLN A 39 SITE 3 AC1 32 LEU A 42 ASP A 43 ILE A 44 THR A 66 SITE 4 AC1 32 ALA A 67 GLY A 68 SER A 69 THR A 90 SITE 5 AC1 32 LYS A 91 THR A 115 SER A 116 PRO A 158 SITE 6 AC1 32 GLY A 159 LEU A 160 THR A 161 THR A 163 SITE 7 AC1 32 ALA A 165 TYR A 166 HOH A 236 HOH A 247 SITE 8 AC1 32 HOH A 273 HOH A 449 HOH A 914 HOH A 988 SITE 1 AC2 31 GLY B 13 THR B 15 SER B 16 GLY B 17 SITE 2 AC2 31 ILE B 18 SER B 37 ARG B 38 GLN B 39 SITE 3 AC2 31 LEU B 42 ASP B 43 ILE B 44 THR B 66 SITE 4 AC2 31 ALA B 67 GLY B 68 SER B 69 THR B 90 SITE 5 AC2 31 LYS B 91 THR B 115 SER B 116 PRO B 158 SITE 6 AC2 31 GLY B 159 LEU B 160 THR B 161 THR B 163 SITE 7 AC2 31 ALA B 165 TYR B 166 HOH B 224 HOH B 252 SITE 8 AC2 31 HOH B 280 HOH B 484 HOH B 989 SITE 1 AC3 31 GLY C 13 THR C 15 SER C 16 GLY C 17 SITE 2 AC3 31 ILE C 18 SER C 37 ARG C 38 GLN C 39 SITE 3 AC3 31 LEU C 42 ASP C 43 ILE C 44 THR C 66 SITE 4 AC3 31 ALA C 67 GLY C 68 SER C 69 THR C 90 SITE 5 AC3 31 LYS C 91 THR C 115 SER C 116 PRO C 158 SITE 6 AC3 31 GLY C 159 LEU C 160 THR C 161 THR C 163 SITE 7 AC3 31 GLU C 164 ALA C 165 TYR C 166 HOH C 235 SITE 8 AC3 31 HOH C 249 HOH C 265 HOH C 458 SITE 1 AC4 34 GLY D 13 THR D 15 SER D 16 GLY D 17 SITE 2 AC4 34 ILE D 18 SER D 37 ARG D 38 GLN D 39 SITE 3 AC4 34 LEU D 42 ASP D 43 ILE D 44 THR D 66 SITE 4 AC4 34 ALA D 67 GLY D 68 SER D 69 THR D 90 SITE 5 AC4 34 LYS D 91 THR D 115 SER D 116 PRO D 158 SITE 6 AC4 34 GLY D 159 LEU D 160 THR D 161 THR D 163 SITE 7 AC4 34 ALA D 165 TYR D 166 HOH D 226 HOH D 239 SITE 8 AC4 34 HOH D 270 HOH D 486 HOH D 612 HOH D 676 SITE 9 AC4 34 HOH D 733 HOH D 987 CRYST1 69.630 96.260 72.110 90.00 103.99 90.00 P 1 21 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 0.014362 0.000000 0.003579 0.00000 SCALE2 0.000000 0.010389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014292 0.00000 MASTER 436 0 4 40 26 0 33 6 0 0 0 72 END