HEADER OXIDOREDUCTASE 07-APR-13 4K22 TITLE STRUCTURE OF THE C-TERMINAL TRUNCATED FORM OF E.COLI C5-HYDROXYLASE TITLE 2 UBII INVOLVED IN UBIQUINONE (Q8) BIOSYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN VISC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-365; COMPND 5 EC: 1.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: VISC, B2906, JW2874; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 KEYWDS ROSSMANN FOLD, HYDROXYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR L.PECQUEUR,M.LOMBARD,B.GOLINELLI-PIMPANEAU,M.FONTECAVE REVDAT 4 20-MAR-24 4K22 1 REMARK REVDAT 3 21-AUG-13 4K22 1 JRNL REVDAT 2 12-JUN-13 4K22 1 REMARK REVDAT 1 29-MAY-13 4K22 0 JRNL AUTH M.H.CHEHADE,L.LOISEAU,M.LOMBARD,L.PECQUEUR,A.ISMAIL, JRNL AUTH 2 M.SMADJA,B.GOLINELLI-PIMPANEAU,C.MELLOT-DRAZNIEKS,O.HAMELIN, JRNL AUTH 3 L.AUSSEL,S.KIEFFER-JAQUINOD,N.LABESSAN,F.BARRAS,M.FONTECAVE, JRNL AUTH 4 F.PIERREL JRNL TITL UBII, A NEW GENE IN ESCHERICHIA COLI COENZYME Q JRNL TITL 2 BIOSYNTHESIS, IS INVOLVED IN AEROBIC C5-HYDROXYLATION. JRNL REF J.BIOL.CHEM. V. 288 20085 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23709220 JRNL DOI 10.1074/JBC.M113.480368 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 57894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2894 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 46.9944 - 5.5150 0.99 2808 147 0.1679 0.1983 REMARK 3 2 5.5150 - 4.3785 1.00 2708 143 0.1411 0.1867 REMARK 3 3 4.3785 - 3.8253 1.00 2653 140 0.1417 0.1459 REMARK 3 4 3.8253 - 3.4756 1.00 2651 139 0.1464 0.1863 REMARK 3 5 3.4756 - 3.2266 1.00 2637 139 0.1498 0.1787 REMARK 3 6 3.2266 - 3.0364 1.00 2625 138 0.1552 0.1788 REMARK 3 7 3.0364 - 2.8844 1.00 2610 137 0.1665 0.2064 REMARK 3 8 2.8844 - 2.7588 1.00 2616 138 0.1706 0.2099 REMARK 3 9 2.7588 - 2.6526 1.00 2600 137 0.1714 0.2177 REMARK 3 10 2.6526 - 2.5611 1.00 2607 137 0.1738 0.2249 REMARK 3 11 2.5611 - 2.4810 1.00 2599 137 0.1736 0.2367 REMARK 3 12 2.4810 - 2.4101 1.00 2622 138 0.1674 0.1991 REMARK 3 13 2.4101 - 2.3467 1.00 2607 137 0.1748 0.1992 REMARK 3 14 2.3467 - 2.2894 1.00 2570 136 0.1738 0.2528 REMARK 3 15 2.2894 - 2.2374 1.00 2590 136 0.1848 0.2382 REMARK 3 16 2.2374 - 2.1897 1.00 2623 138 0.1865 0.2111 REMARK 3 17 2.1897 - 2.1459 1.00 2567 135 0.1888 0.2437 REMARK 3 18 2.1459 - 2.1054 1.00 2595 137 0.2014 0.2677 REMARK 3 19 2.1054 - 2.0678 1.00 2583 136 0.2110 0.2522 REMARK 3 20 2.0678 - 2.0328 1.00 2589 136 0.2275 0.2705 REMARK 3 21 2.0328 - 2.0000 0.99 2540 133 0.2493 0.2997 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.20 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.15 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 : 0.012 5787 REMARK 3 ANGLE : 1.253 7840 REMARK 3 CHIRALITY : 0.055 848 REMARK 3 PLANARITY : 0.008 1028 REMARK 3 DIHEDRAL : 14.102 2109 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 1:140 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5495 17.7978 -24.0577 REMARK 3 T TENSOR REMARK 3 T11: 0.2220 T22: 0.2624 REMARK 3 T33: 0.2322 T12: 0.0517 REMARK 3 T13: 0.0275 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 1.6336 L22: 3.6789 REMARK 3 L33: 1.6718 L12: 0.4764 REMARK 3 L13: -0.1310 L23: 0.8424 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: -0.2107 S13: -0.0327 REMARK 3 S21: 0.5928 S22: -0.0479 S23: 0.3671 REMARK 3 S31: 0.1739 S32: -0.0280 S33: 0.0773 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 141:363 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5550 16.0190 -30.5627 REMARK 3 T TENSOR REMARK 3 T11: 0.1541 T22: 0.2002 REMARK 3 T33: 0.1659 T12: 0.0498 REMARK 3 T13: 0.0042 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.9513 L22: 3.3466 REMARK 3 L33: 1.1813 L12: 0.5599 REMARK 3 L13: 0.2473 L23: 1.1176 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: -0.1299 S13: 0.0181 REMARK 3 S21: 0.2274 S22: 0.0900 S23: -0.0016 REMARK 3 S31: 0.1189 S32: 0.0505 S33: -0.0370 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND (RESID 2:140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8083 24.7440 -61.6267 REMARK 3 T TENSOR REMARK 3 T11: 0.3786 T22: 0.3848 REMARK 3 T33: 0.2188 T12: -0.1137 REMARK 3 T13: -0.0185 T23: 0.0591 REMARK 3 L TENSOR REMARK 3 L11: 2.7833 L22: 1.5306 REMARK 3 L33: 1.4978 L12: -0.9941 REMARK 3 L13: -0.5366 L23: 0.3147 REMARK 3 S TENSOR REMARK 3 S11: 0.1162 S12: 0.6736 S13: 0.1588 REMARK 3 S21: -0.4243 S22: -0.1272 S23: -0.1247 REMARK 3 S31: -0.2085 S32: -0.0962 S33: -0.0124 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 141:362 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8931 18.6360 -54.9824 REMARK 3 T TENSOR REMARK 3 T11: 0.2853 T22: 0.2622 REMARK 3 T33: 0.1644 T12: -0.0517 REMARK 3 T13: 0.0050 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 2.6226 L22: 1.2455 REMARK 3 L33: 0.6926 L12: -0.8110 REMARK 3 L13: 0.3436 L23: 0.0757 REMARK 3 S TENSOR REMARK 3 S11: 0.0654 S12: 0.3448 S13: -0.0337 REMARK 3 S21: -0.2374 S22: -0.0227 S23: 0.0086 REMARK 3 S31: -0.0694 S32: -0.0861 S33: -0.0506 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MODEL CALCULATED FROM EXPERIMENTAL PHASES DERIVED BY SAD WITH REMARK 3 SELENOMETHIONYLATED PROTEIN. REMARK 3 DATA USED FOR SAD PHASING STORED IN CRYSTAL2 DATASET. REMARK 3 DATA FOR MR AND REFINEMENT TO 2.0 A RESOLUTION STORED IN CRYSTAL1 REMARK 3 DATASET' REMARK 4 REMARK 4 4K22 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-12; 14-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5; 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SOLEIL; SOLEIL REMARK 200 BEAMLINE : PROXIMA 1; PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.980110; 0.979180 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M; PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58014 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06660 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD THEN MR REMARK 200 SOFTWARE USED: PHASER 2.5.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5, 12% PEG 4000, 0.1M REMARK 280 NACL, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292K. 0.1M BISTRIS-PROPANE PH 9.0, 14% PEG 4000, 0.1M NACL, REMARK 280 0.15M MGCL2', VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 47.36500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.36500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.07000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 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 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 VAL A 36 REMARK 465 GLN A 37 REMARK 465 GLU A 38 REMARK 465 PRO A 39 REMARK 465 LEU A 40 REMARK 465 ALA A 41 REMARK 465 ALA A 42 REMARK 465 ASN A 43 REMARK 465 ALA A 44 REMARK 465 LYS A 364 REMARK 465 LYS A 365 REMARK 465 MET B 1 REMARK 465 ARG B 35 REMARK 465 VAL B 36 REMARK 465 GLN B 37 REMARK 465 GLU B 38 REMARK 465 PRO B 39 REMARK 465 LEU B 40 REMARK 465 ALA B 41 REMARK 465 ALA B 42 REMARK 465 ALA B 363 REMARK 465 LYS B 364 REMARK 465 LYS B 365 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 35 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 137 CG CD OE1 NE2 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 B 679 O HOH B 774 1.88 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 ARG B 321 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 321 NE - CZ - NH2 ANGL. DEV. = -4.0 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 ARG A 73 -70.28 -74.49 REMARK 500 ALA A 133 51.67 -147.45 REMARK 500 HIS A 292 -102.02 -117.96 REMARK 500 ARG B 73 -70.68 -74.09 REMARK 500 ARG B 73 -70.68 -62.81 REMARK 500 ALA B 133 49.15 -147.79 REMARK 500 HIS B 292 -100.45 -117.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG B 321 14.98 REMARK 500 ARG B 321 13.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 505 REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN EXPRESSED WITH A C-TERMINAL HIS-TAG. PRIOR TO REMARK 999 CRYSTALLISATION, UBII WAS SUBJECTED TO LIMITED PROTEOLYSIS WITH REMARK 999 TRYPSIN. TWO CLEAVAGE SITES WERE IDENTIFIED BY MASS SPECTROMETRY TO REMARK 999 BE LOCATED AT THE C-TERMINAL OF RESIDUE LYS 364 AND LYS 365. THE C- REMARK 999 TERMINAL FRAGMENT (34 RESIDUES) CONTAINING THE HIS-TAG WAS REMOVED REMARK 999 BY NI-NTA PURIFICATION. DBREF 4K22 A 1 365 UNP P25535 VISC_ECOLI 1 365 DBREF 4K22 B 1 365 UNP P25535 VISC_ECOLI 1 365 SEQRES 1 A 365 MET GLN SER VAL ASP VAL ALA ILE VAL GLY GLY GLY MET SEQRES 2 A 365 VAL GLY LEU ALA VAL ALA CYS GLY LEU GLN GLY SER GLY SEQRES 3 A 365 LEU ARG VAL ALA VAL LEU GLU GLN ARG VAL GLN GLU PRO SEQRES 4 A 365 LEU ALA ALA ASN ALA PRO PRO GLN LEU ARG VAL SER ALA SEQRES 5 A 365 ILE ASN ALA ALA SER GLU LYS LEU LEU THR ARG LEU GLY SEQRES 6 A 365 VAL TRP GLN ASP ILE LEU SER ARG ARG ALA SER CYS TYR SEQRES 7 A 365 HIS GLY MET GLU VAL TRP ASP LYS ASP SER PHE GLY HIS SEQRES 8 A 365 ILE SER PHE ASP ASP GLN SER MET GLY TYR SER HIS LEU SEQRES 9 A 365 GLY HIS ILE VAL GLU ASN SER VAL ILE HIS TYR ALA LEU SEQRES 10 A 365 TRP ASN LYS ALA HIS GLN SER SER ASP ILE THR LEU LEU SEQRES 11 A 365 ALA PRO ALA GLU LEU GLN GLN VAL ALA TRP GLY GLU ASN SEQRES 12 A 365 GLU THR PHE LEU THR LEU LYS ASP GLY SER MET LEU THR SEQRES 13 A 365 ALA ARG LEU VAL ILE GLY ALA ASP GLY ALA ASN SER TRP SEQRES 14 A 365 LEU ARG ASN LYS ALA ASP ILE PRO LEU THR PHE TRP ASP SEQRES 15 A 365 TYR GLN HIS HIS ALA LEU VAL ALA THR ILE ARG THR GLU SEQRES 16 A 365 GLU PRO HIS ASP ALA VAL ALA ARG GLN VAL PHE HIS GLY SEQRES 17 A 365 GLU GLY ILE LEU ALA PHE LEU PRO LEU SER ASP PRO HIS SEQRES 18 A 365 LEU CYS SER ILE VAL TRP SER LEU SER PRO GLU GLU ALA SEQRES 19 A 365 GLN ARG MET GLN GLN ALA SER GLU ASP GLU PHE ASN ARG SEQRES 20 A 365 ALA LEU ASN ILE ALA PHE ASP ASN ARG LEU GLY LEU CYS SEQRES 21 A 365 LYS VAL GLU SER ALA ARG GLN VAL PHE PRO LEU THR GLY SEQRES 22 A 365 ARG TYR ALA ARG GLN PHE ALA SER HIS ARG LEU ALA LEU SEQRES 23 A 365 VAL GLY ASP ALA ALA HIS THR ILE HIS PRO LEU ALA GLY SEQRES 24 A 365 GLN GLY VAL ASN LEU GLY PHE MET ASP ALA ALA GLU LEU SEQRES 25 A 365 ILE ALA GLU LEU LYS ARG LEU HIS ARG GLN GLY LYS ASP SEQRES 26 A 365 ILE GLY GLN TYR ILE TYR LEU ARG ARG TYR GLU ARG SER SEQRES 27 A 365 ARG LYS HIS SER ALA ALA LEU MET LEU ALA GLY MET GLN SEQRES 28 A 365 GLY PHE ARG ASP LEU PHE SER GLY THR ASN PRO ALA LYS SEQRES 29 A 365 LYS SEQRES 1 B 365 MET GLN SER VAL ASP VAL ALA ILE VAL GLY GLY GLY MET SEQRES 2 B 365 VAL GLY LEU ALA VAL ALA CYS GLY LEU GLN GLY SER GLY SEQRES 3 B 365 LEU ARG VAL ALA VAL LEU GLU GLN ARG VAL GLN GLU PRO SEQRES 4 B 365 LEU ALA ALA ASN ALA PRO PRO GLN LEU ARG VAL SER ALA SEQRES 5 B 365 ILE ASN ALA ALA SER GLU LYS LEU LEU THR ARG LEU GLY SEQRES 6 B 365 VAL TRP GLN ASP ILE LEU SER ARG ARG ALA SER CYS TYR SEQRES 7 B 365 HIS GLY MET GLU VAL TRP ASP LYS ASP SER PHE GLY HIS SEQRES 8 B 365 ILE SER PHE ASP ASP GLN SER MET GLY TYR SER HIS LEU SEQRES 9 B 365 GLY HIS ILE VAL GLU ASN SER VAL ILE HIS TYR ALA LEU SEQRES 10 B 365 TRP ASN LYS ALA HIS GLN SER SER ASP ILE THR LEU LEU SEQRES 11 B 365 ALA PRO ALA GLU LEU GLN GLN VAL ALA TRP GLY GLU ASN SEQRES 12 B 365 GLU THR PHE LEU THR LEU LYS ASP GLY SER MET LEU THR SEQRES 13 B 365 ALA ARG LEU VAL ILE GLY ALA ASP GLY ALA ASN SER TRP SEQRES 14 B 365 LEU ARG ASN LYS ALA ASP ILE PRO LEU THR PHE TRP ASP SEQRES 15 B 365 TYR GLN HIS HIS ALA LEU VAL ALA THR ILE ARG THR GLU SEQRES 16 B 365 GLU PRO HIS ASP ALA VAL ALA ARG GLN VAL PHE HIS GLY SEQRES 17 B 365 GLU GLY ILE LEU ALA PHE LEU PRO LEU SER ASP PRO HIS SEQRES 18 B 365 LEU CYS SER ILE VAL TRP SER LEU SER PRO GLU GLU ALA SEQRES 19 B 365 GLN ARG MET GLN GLN ALA SER GLU ASP GLU PHE ASN ARG SEQRES 20 B 365 ALA LEU ASN ILE ALA PHE ASP ASN ARG LEU GLY LEU CYS SEQRES 21 B 365 LYS VAL GLU SER ALA ARG GLN VAL PHE PRO LEU THR GLY SEQRES 22 B 365 ARG TYR ALA ARG GLN PHE ALA SER HIS ARG LEU ALA LEU SEQRES 23 B 365 VAL GLY ASP ALA ALA HIS THR ILE HIS PRO LEU ALA GLY SEQRES 24 B 365 GLN GLY VAL ASN LEU GLY PHE MET ASP ALA ALA GLU LEU SEQRES 25 B 365 ILE ALA GLU LEU LYS ARG LEU HIS ARG GLN GLY LYS ASP SEQRES 26 B 365 ILE GLY GLN TYR ILE TYR LEU ARG ARG TYR GLU ARG SER SEQRES 27 B 365 ARG LYS HIS SER ALA ALA LEU MET LEU ALA GLY MET GLN SEQRES 28 B 365 GLY PHE ARG ASP LEU PHE SER GLY THR ASN PRO ALA LYS SEQRES 29 B 365 LYS HET GOL A 501 6 HET GOL A 502 6 HET CL A 503 1 HET PEG A 504 7 HET GOL A 505 6 HET CL A 506 1 HET GOL A 507 6 HET GOL B 501 6 HET CL B 502 1 HET CL B 503 1 HET GOL B 504 6 HET GOL B 505 6 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 7(C3 H8 O3) FORMUL 5 CL 4(CL 1-) FORMUL 6 PEG C4 H10 O3 FORMUL 15 HOH *493(H2 O) HELIX 1 1 GLY A 12 GLN A 23 1 12 HELIX 2 2 ASN A 54 LEU A 64 1 11 HELIX 3 3 VAL A 66 ARG A 74 1 9 HELIX 4 4 GLN A 97 GLY A 100 5 4 HELIX 5 5 ASN A 110 GLN A 123 1 14 HELIX 6 6 ASN A 167 ALA A 174 1 8 HELIX 7 7 SER A 230 ALA A 240 1 11 HELIX 8 8 SER A 241 PHE A 253 1 13 HELIX 9 9 PRO A 296 GLN A 300 5 5 HELIX 10 10 GLY A 301 GLN A 322 1 22 HELIX 11 11 GLN A 328 ALA A 348 1 21 HELIX 12 12 GLN A 351 PHE A 357 1 7 HELIX 13 13 GLY B 12 GLN B 23 1 12 HELIX 14 14 ASN B 54 LEU B 64 1 11 HELIX 15 15 VAL B 66 ARG B 74 1 9 HELIX 16 16 GLN B 97 GLY B 100 5 4 HELIX 17 17 ASN B 110 GLN B 123 1 14 HELIX 18 18 ASN B 167 ASP B 175 1 9 HELIX 19 19 SER B 230 ALA B 240 1 11 HELIX 20 20 SER B 241 PHE B 253 1 13 HELIX 21 21 PRO B 296 GLN B 300 5 5 HELIX 22 22 GLY B 301 GLN B 322 1 22 HELIX 23 23 GLN B 328 ALA B 348 1 21 HELIX 24 24 GLN B 351 PHE B 357 1 7 SHEET 1 A 6 ILE A 127 LEU A 130 0 SHEET 2 A 6 VAL A 29 LEU A 32 1 N VAL A 31 O LEU A 130 SHEET 3 A 6 GLN A 2 VAL A 9 1 N ILE A 8 O ALA A 30 SHEET 4 A 6 MET A 154 GLY A 162 1 O ILE A 161 N VAL A 9 SHEET 5 A 6 THR A 145 LEU A 149 -1 N LEU A 147 O LEU A 155 SHEET 6 A 6 LEU A 135 TRP A 140 -1 N GLN A 136 O THR A 148 SHEET 1 B 6 ILE A 127 LEU A 130 0 SHEET 2 B 6 VAL A 29 LEU A 32 1 N VAL A 31 O LEU A 130 SHEET 3 B 6 GLN A 2 VAL A 9 1 N ILE A 8 O ALA A 30 SHEET 4 B 6 MET A 154 GLY A 162 1 O ILE A 161 N VAL A 9 SHEET 5 B 6 LEU A 284 LEU A 286 1 O ALA A 285 N GLY A 162 SHEET 6 B 6 ALA A 280 SER A 281 -1 N SER A 281 O LEU A 284 SHEET 1 C 3 VAL A 50 ILE A 53 0 SHEET 2 C 3 GLY A 105 GLU A 109 -1 O HIS A 106 N ILE A 53 SHEET 3 C 3 SER A 76 TYR A 78 -1 N SER A 76 O ILE A 107 SHEET 1 D 7 HIS A 91 ASP A 95 0 SHEET 2 D 7 GLY A 80 ASP A 85 -1 N VAL A 83 O ILE A 92 SHEET 3 D 7 VAL A 201 HIS A 207 1 O PHE A 206 N TRP A 84 SHEET 4 D 7 GLY A 210 PRO A 216 -1 O PHE A 214 N ARG A 203 SHEET 5 D 7 LEU A 222 LEU A 229 -1 O SER A 224 N LEU A 215 SHEET 6 D 7 THR A 179 THR A 194 -1 N ILE A 192 O CYS A 223 SHEET 7 D 7 CYS A 260 VAL A 262 -1 O LYS A 261 N ARG A 193 SHEET 1 E 7 HIS A 91 ASP A 95 0 SHEET 2 E 7 GLY A 80 ASP A 85 -1 N VAL A 83 O ILE A 92 SHEET 3 E 7 VAL A 201 HIS A 207 1 O PHE A 206 N TRP A 84 SHEET 4 E 7 GLY A 210 PRO A 216 -1 O PHE A 214 N ARG A 203 SHEET 5 E 7 LEU A 222 LEU A 229 -1 O SER A 224 N LEU A 215 SHEET 6 E 7 THR A 179 THR A 194 -1 N ILE A 192 O CYS A 223 SHEET 7 E 7 GLN A 267 TYR A 275 -1 O GLY A 273 N TRP A 181 SHEET 1 F 6 ILE B 127 LEU B 130 0 SHEET 2 F 6 VAL B 29 LEU B 32 1 N VAL B 31 O LEU B 130 SHEET 3 F 6 SER B 3 VAL B 9 1 N ILE B 8 O ALA B 30 SHEET 4 F 6 MET B 154 GLY B 162 1 O ILE B 161 N VAL B 9 SHEET 5 F 6 THR B 145 LEU B 149 -1 N LEU B 147 O LEU B 155 SHEET 6 F 6 LEU B 135 TRP B 140 -1 N GLN B 136 O THR B 148 SHEET 1 G 6 ILE B 127 LEU B 130 0 SHEET 2 G 6 VAL B 29 LEU B 32 1 N VAL B 31 O LEU B 130 SHEET 3 G 6 SER B 3 VAL B 9 1 N ILE B 8 O ALA B 30 SHEET 4 G 6 MET B 154 GLY B 162 1 O ILE B 161 N VAL B 9 SHEET 5 G 6 LEU B 284 LEU B 286 1 O ALA B 285 N GLY B 162 SHEET 6 G 6 ALA B 280 SER B 281 -1 N SER B 281 O LEU B 284 SHEET 1 H 3 VAL B 50 ILE B 53 0 SHEET 2 H 3 GLY B 105 GLU B 109 -1 O HIS B 106 N ILE B 53 SHEET 3 H 3 SER B 76 TYR B 78 -1 N SER B 76 O ILE B 107 SHEET 1 I 7 HIS B 91 ASP B 95 0 SHEET 2 I 7 GLY B 80 ASP B 85 -1 N VAL B 83 O ILE B 92 SHEET 3 I 7 VAL B 201 HIS B 207 1 O PHE B 206 N TRP B 84 SHEET 4 I 7 GLY B 210 PRO B 216 -1 O LEU B 212 N VAL B 205 SHEET 5 I 7 LEU B 222 LEU B 229 -1 O SER B 224 N LEU B 215 SHEET 6 I 7 THR B 179 THR B 194 -1 N ILE B 192 O CYS B 223 SHEET 7 I 7 CYS B 260 VAL B 262 -1 O LYS B 261 N ARG B 193 SHEET 1 J 7 HIS B 91 ASP B 95 0 SHEET 2 J 7 GLY B 80 ASP B 85 -1 N VAL B 83 O ILE B 92 SHEET 3 J 7 VAL B 201 HIS B 207 1 O PHE B 206 N TRP B 84 SHEET 4 J 7 GLY B 210 PRO B 216 -1 O LEU B 212 N VAL B 205 SHEET 5 J 7 LEU B 222 LEU B 229 -1 O SER B 224 N LEU B 215 SHEET 6 J 7 THR B 179 THR B 194 -1 N ILE B 192 O CYS B 223 SHEET 7 J 7 GLN B 267 TYR B 275 -1 O GLY B 273 N TRP B 181 CISPEP 1 ALA A 131 PRO A 132 0 -1.42 CISPEP 2 HIS A 295 PRO A 296 0 -1.82 CISPEP 3 HIS B 295 PRO B 296 0 -3.16 SITE 1 AC1 8 ARG A 49 VAL A 226 PHE A 269 GLN A 300 SITE 2 AC1 8 GOL A 507 HOH A 632 HOH A 706 HOH A 707 SITE 1 AC2 6 TYR A 329 ARG A 333 TRP B 140 ALA B 174 SITE 2 AC2 6 SER B 281 HIS B 282 SITE 1 AC3 3 GLY A 65 TRP A 67 GLN A 68 SITE 1 AC4 3 TRP A 84 ASP A 254 ARG A 256 SITE 1 AC5 7 GLN A 204 HIS A 295 PRO A 296 LEU A 297 SITE 2 AC5 7 ALA A 298 HOH A 677 HOH A 845 SITE 1 AC6 6 ASP A 175 TRP A 181 ASP A 182 HOH A 601 SITE 2 AC6 6 HOH A 702 ARG B 277 SITE 1 AC7 4 PRO A 270 THR A 272 GOL A 501 HOH A 612 SITE 1 AC8 6 GLN B 204 HIS B 295 PRO B 296 LEU B 297 SITE 2 AC8 6 ALA B 298 HOH B 755 SITE 1 AC9 4 GLN A 328 ILE A 330 TYR B 329 ILE B 330 SITE 1 BC1 3 GLY B 65 TRP B 67 GLN B 68 SITE 1 BC2 9 ARG B 49 VAL B 226 PHE B 269 ILE B 294 SITE 2 BC2 9 GLN B 300 GOL B 505 HOH B 637 HOH B 662 SITE 3 BC2 9 HOH B 710 SITE 1 BC3 5 PRO B 270 LEU B 271 THR B 272 GOL B 504 SITE 2 BC3 5 HOH B 628 CRYST1 94.730 124.140 71.890 90.00 90.00 90.00 P 21 21 2 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 0.010556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013910 0.00000