HEADER OXIDOREDUCTASE 12-SEP-13 4MPD TITLE STAPHYLOFERRIN B PRECURSOR BIOSYNTHETIC ENZYME SBNB BOUND A- TITLE 2 KETOGLUTARATE AND NAD+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ORNITHINE CYCLODEAMINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 196620; SOURCE 4 STRAIN: NEWMAN; SOURCE 5 GENE: SBNB; 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: PET28A KEYWDS SIDEROPHORE, IRON, L-DAP SYNTHESIS, ACEGA DEHYDROGENASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.KOBYLARZ,M.E.P.MURPHY REVDAT 4 28-FEB-24 4MPD 1 REMARK SEQADV REVDAT 3 15-NOV-17 4MPD 1 REMARK REVDAT 2 09-APR-14 4MPD 1 JRNL REVDAT 1 05-MAR-14 4MPD 0 JRNL AUTH M.J.KOBYLARZ,J.C.GRIGG,S.J.TAKAYAMA,D.K.RAI,D.E.HEINRICHS, JRNL AUTH 2 M.E.MURPHY JRNL TITL SYNTHESIS OF L-2,3-DIAMINOPROPIONIC ACID, A SIDEROPHORE AND JRNL TITL 2 ANTIBIOTIC PRECURSOR. JRNL REF CHEM.BIOL. V. 21 379 2014 JRNL REFN ISSN 1074-5521 JRNL PMID 24485762 JRNL DOI 10.1016/J.CHEMBIOL.2013.12.011 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 15406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1505 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 27.2510 - 4.6652 0.98 1588 173 0.2129 0.2769 REMARK 3 2 4.6652 - 3.7059 0.91 1366 159 0.1918 0.2192 REMARK 3 3 3.7059 - 3.2383 0.74 1112 115 0.2147 0.2190 REMARK 3 4 3.2383 - 2.9426 0.75 1114 114 0.2473 0.2873 REMARK 3 5 2.9426 - 2.7319 0.76 1119 117 0.2761 0.3525 REMARK 3 6 2.7319 - 2.5710 0.81 1164 123 0.2720 0.2916 REMARK 3 7 2.5710 - 2.4423 0.83 1224 131 0.2435 0.2695 REMARK 3 8 2.4423 - 2.3360 0.88 1264 135 0.2607 0.3089 REMARK 3 9 2.3360 - 2.2461 0.91 1300 147 0.2578 0.3144 REMARK 3 10 2.2461 - 2.1687 0.92 1318 147 0.2491 0.2656 REMARK 3 11 2.1687 - 2.1009 0.93 1332 144 0.2632 0.2819 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.10 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 : 0.003 2622 REMARK 3 ANGLE : 0.701 3557 REMARK 3 CHIRALITY : 0.052 400 REMARK 3 PLANARITY : 0.002 459 REMARK 3 DIHEDRAL : 14.472 974 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.8292 22.7176 -11.1396 REMARK 3 T TENSOR REMARK 3 T11: 0.2646 T22: 0.2544 REMARK 3 T33: 0.1945 T12: -0.0188 REMARK 3 T13: -0.0736 T23: 0.0467 REMARK 3 L TENSOR REMARK 3 L11: 4.6259 L22: 1.3836 REMARK 3 L33: 2.6032 L12: 0.4307 REMARK 3 L13: -2.0719 L23: 0.1900 REMARK 3 S TENSOR REMARK 3 S11: -0.1783 S12: 0.4600 S13: -0.1222 REMARK 3 S21: 0.2006 S22: 0.0075 S23: -0.1740 REMARK 3 S31: -0.1580 S32: -0.0732 S33: 0.1469 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4648 37.1148 -3.4940 REMARK 3 T TENSOR REMARK 3 T11: 0.3440 T22: 0.3679 REMARK 3 T33: 0.6061 T12: 0.0005 REMARK 3 T13: -0.0751 T23: 0.0569 REMARK 3 L TENSOR REMARK 3 L11: 1.1951 L22: 0.5235 REMARK 3 L33: 5.8302 L12: 0.5641 REMARK 3 L13: -1.6147 L23: -1.3137 REMARK 3 S TENSOR REMARK 3 S11: -0.0241 S12: -0.0666 S13: 0.4512 REMARK 3 S21: 0.1545 S22: -0.1437 S23: -0.1790 REMARK 3 S31: -0.1259 S32: 1.3235 S33: -0.2335 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.3032 28.3224 0.8709 REMARK 3 T TENSOR REMARK 3 T11: 0.2111 T22: 0.2379 REMARK 3 T33: 0.3925 T12: 0.0455 REMARK 3 T13: -0.0608 T23: -0.0437 REMARK 3 L TENSOR REMARK 3 L11: 4.8125 L22: 2.8915 REMARK 3 L33: 3.4030 L12: -0.4976 REMARK 3 L13: -0.1468 L23: 0.4084 REMARK 3 S TENSOR REMARK 3 S11: 0.0073 S12: -0.3267 S13: 0.3718 REMARK 3 S21: 0.2509 S22: -0.0432 S23: -0.7988 REMARK 3 S31: 0.0485 S32: 0.2422 S33: 0.0105 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 253 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0589 17.4892 -3.7425 REMARK 3 T TENSOR REMARK 3 T11: 0.1955 T22: 0.1618 REMARK 3 T33: 0.1858 T12: 0.0337 REMARK 3 T13: -0.0016 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 3.7247 L22: 3.2522 REMARK 3 L33: 1.6543 L12: 0.4370 REMARK 3 L13: 0.2549 L23: -0.0639 REMARK 3 S TENSOR REMARK 3 S11: -0.0671 S12: -0.1171 S13: -0.3225 REMARK 3 S21: 0.1874 S22: 0.1064 S23: 0.0195 REMARK 3 S31: 0.1030 S32: 0.0632 S33: -0.0423 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 254 THROUGH 283 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3787 40.0122 -6.4844 REMARK 3 T TENSOR REMARK 3 T11: 0.4083 T22: 0.2865 REMARK 3 T33: 0.3835 T12: 0.0728 REMARK 3 T13: -0.0300 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 3.6470 L22: 3.8241 REMARK 3 L33: 5.4206 L12: 2.0869 REMARK 3 L13: 4.1164 L23: 3.2546 REMARK 3 S TENSOR REMARK 3 S11: -0.1979 S12: -0.2505 S13: 0.4449 REMARK 3 S21: -0.4253 S22: 0.0458 S23: 0.0951 REMARK 3 S31: -0.9352 S32: -0.2530 S33: 0.1985 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 284 THROUGH 301 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8574 28.3628 -19.1721 REMARK 3 T TENSOR REMARK 3 T11: 0.3172 T22: 0.3722 REMARK 3 T33: 0.1691 T12: -0.0055 REMARK 3 T13: 0.0314 T23: 0.0396 REMARK 3 L TENSOR REMARK 3 L11: 5.9268 L22: 4.1038 REMARK 3 L33: 4.3007 L12: -0.8634 REMARK 3 L13: 3.0019 L23: -0.0830 REMARK 3 S TENSOR REMARK 3 S11: 0.1575 S12: 0.8231 S13: 0.7393 REMARK 3 S21: -0.8428 S22: -0.4238 S23: -0.2998 REMARK 3 S31: -0.0002 S32: 0.7431 S33: 0.2066 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 302 THROUGH 336 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.8811 26.3609 -10.1542 REMARK 3 T TENSOR REMARK 3 T11: 0.2672 T22: 0.2840 REMARK 3 T33: 0.3474 T12: -0.0251 REMARK 3 T13: -0.0166 T23: 0.0675 REMARK 3 L TENSOR REMARK 3 L11: 2.4581 L22: -0.2681 REMARK 3 L33: 0.5527 L12: -1.0892 REMARK 3 L13: -0.8953 L23: 0.5095 REMARK 3 S TENSOR REMARK 3 S11: 0.0311 S12: 0.3358 S13: 0.4762 REMARK 3 S21: -0.0586 S22: -0.0736 S23: -0.0168 REMARK 3 S31: 0.1416 S32: -0.1289 S33: 0.0055 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 4MPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX VHF REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 27.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.3, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 0.2 M MGCL2, 29-33% PEG REMARK 280 400, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 75.85900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.96550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.96550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.92950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.96550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.96550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.78850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.96550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.96550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.92950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.96550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.96550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.78850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.85900 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: 7370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 0.000000 1.000000 0.000000 -61.93100 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 61.93100 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ASP A 51 REMARK 465 PRO A 52 REMARK 465 GLU A 53 REMARK 465 ASN A 54 REMARK 465 GLY A 55 REMARK 465 HIS A 56 REMARK 465 ILE A 57 REMARK 465 GLY A 69 REMARK 465 GLY A 70 REMARK 465 GLU A 71 REMARK 465 HIS A 72 REMARK 465 ALA A 73 REMARK 465 ARG A 261 REMARK 465 GLU A 262 REMARK 465 LYS A 263 REMARK 465 LYS A 264 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 ASN A 107 0.66 59.40 REMARK 500 TYR A 220 -27.16 -141.50 REMARK 500 ILE A 237 -56.35 69.14 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 NAJ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4M54 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH N-(1-AMINO-1-CARBOXYL-2-ETHYL)- REMARK 900 GLUTAMIC ACID AND NADH REMARK 900 RELATED ID: 4MP3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN APO SELENOMETHIONINE REMARK 900 RELATED ID: 4MP6 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CITRATE AND NAD+ REMARK 900 RELATED ID: 4MP8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH MALONATE AND NAD+ DBREF 4MPD A 1 336 UNP Q8NYS7 Q8NYS7_STAAW 1 336 SEQADV 4MPD GLY A -2 UNP Q8NYS7 EXPRESSION TAG SEQADV 4MPD SER A -1 UNP Q8NYS7 EXPRESSION TAG SEQADV 4MPD HIS A 0 UNP Q8NYS7 EXPRESSION TAG SEQRES 1 A 339 GLY SER HIS MET ASN ARG GLU MET LEU TYR LEU ASN ARG SEQRES 2 A 339 SER ASP ILE GLU GLN ALA GLY GLY ASN HIS SER GLN VAL SEQRES 3 A 339 TYR VAL ASP ALA LEU THR GLU ALA LEU THR ALA HIS ALA SEQRES 4 A 339 HIS ASN ASP PHE VAL GLN PRO LEU LYS PRO TYR LEU ARG SEQRES 5 A 339 GLN ASP PRO GLU ASN GLY HIS ILE ALA ASP ARG ILE ILE SEQRES 6 A 339 ALA MET PRO SER HIS ILE GLY GLY GLU HIS ALA ILE SER SEQRES 7 A 339 GLY ILE LYS TRP ILE GLY SER LYS HIS ASP ASN PRO SER SEQRES 8 A 339 LYS ARG ASN MET GLU ARG ALA SER GLY VAL ILE ILE LEU SEQRES 9 A 339 ASN ASP PRO GLU THR ASN TYR PRO ILE ALA VAL MET GLU SEQRES 10 A 339 ALA SER LEU ILE SER SER MET ARG THR ALA ALA VAL SER SEQRES 11 A 339 VAL ILE ALA ALA LYS HIS LEU ALA LYS LYS GLY PHE LYS SEQRES 12 A 339 ASP LEU THR ILE ILE GLY CYS GLY LEU ILE GLY ASP LYS SEQRES 13 A 339 GLN LEU GLN SER MET LEU GLU GLN PHE ASP HIS ILE GLU SEQRES 14 A 339 ARG VAL PHE VAL TYR ASP GLN PHE SER GLU ALA CYS ALA SEQRES 15 A 339 ARG PHE VAL ASP ARG TRP GLN GLN GLN ARG PRO GLU ILE SEQRES 16 A 339 ASN PHE ILE ALA THR GLU ASN ALA LYS GLU ALA VAL SER SEQRES 17 A 339 ASN GLY GLU VAL VAL ILE THR CYS THR VAL THR ASP GLN SEQRES 18 A 339 PRO TYR ILE GLU TYR ASP TRP LEU GLN LYS GLY ALA PHE SEQRES 19 A 339 ILE SER ASN ILE SER ILE MET ASP VAL HIS LYS GLU VAL SEQRES 20 A 339 PHE ILE LYS ALA ASP LYS VAL VAL VAL ASP ASP TRP SER SEQRES 21 A 339 GLN CYS ASN ARG GLU LYS LYS THR ILE ASN GLN LEU VAL SEQRES 22 A 339 LEU GLU GLY LYS PHE SER LYS GLU ALA LEU HIS ALA GLU SEQRES 23 A 339 LEU GLY GLN LEU VAL THR GLY ASP ILE PRO GLY ARG GLU SEQRES 24 A 339 ASP ASP ASP GLU ILE ILE LEU LEU ASN PRO MET GLY MET SEQRES 25 A 339 ALA ILE GLU ASP ILE SER SER ALA TYR PHE ILE TYR GLN SEQRES 26 A 339 GLN ALA GLN GLN GLN ASN ILE GLY THR THR LEU ASN LEU SEQRES 27 A 339 TYR HET NAJ A 401 44 HET AKG A 402 10 HETNAM NAJ NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 NAJ C21 H27 N7 O14 P2 FORMUL 3 AKG C5 H6 O5 FORMUL 4 HOH *75(H2 O) HELIX 1 1 ASN A 9 ALA A 16 1 8 HELIX 2 2 HIS A 20 HIS A 37 1 18 HELIX 3 3 HIS A 84 ARG A 90 1 7 HELIX 4 4 ALA A 115 ALA A 135 1 21 HELIX 5 5 GLY A 148 PHE A 162 1 15 HELIX 6 6 PHE A 174 ARG A 189 1 16 HELIX 7 7 ASN A 199 ASN A 206 1 8 HELIX 8 8 GLU A 222 LEU A 226 5 5 HELIX 9 9 HIS A 241 ALA A 248 1 8 HELIX 10 10 ASP A 255 ASN A 260 1 6 HELIX 11 11 ILE A 266 GLU A 272 1 7 HELIX 12 12 LEU A 284 THR A 289 1 6 HELIX 13 13 MET A 309 GLN A 327 1 19 SHEET 1 A 7 TYR A 47 LEU A 48 0 SHEET 2 A 7 ARG A 60 SER A 66 -1 O ILE A 61 N LEU A 48 SHEET 3 A 7 SER A 75 SER A 82 -1 O SER A 82 N ARG A 60 SHEET 4 A 7 ALA A 95 ASN A 102 -1 O SER A 96 N GLY A 81 SHEET 5 A 7 PRO A 109 GLU A 114 -1 O ILE A 110 N LEU A 101 SHEET 6 A 7 GLU A 4 LEU A 8 1 N LEU A 8 O VAL A 112 SHEET 7 A 7 THR A 331 ASN A 334 -1 O LEU A 333 N MET A 5 SHEET 1 B 8 ASN A 193 ALA A 196 0 SHEET 2 B 8 ARG A 167 TYR A 171 1 N VAL A 170 O ILE A 195 SHEET 3 B 8 ASP A 141 ILE A 145 1 N ILE A 144 O PHE A 169 SHEET 4 B 8 VAL A 209 THR A 212 1 O VAL A 209 N THR A 143 SHEET 5 B 8 PHE A 231 SER A 233 1 O SER A 233 N VAL A 210 SHEET 6 B 8 ILE A 302 ASN A 305 1 O LEU A 304 N ILE A 232 SHEET 7 B 8 LYS A 250 VAL A 253 1 N VAL A 252 O ASN A 305 SHEET 8 B 8 ALA A 282 GLU A 283 1 O ALA A 282 N VAL A 253 SITE 1 AC1 23 ARG A 60 ARG A 94 ARG A 122 THR A 123 SITE 2 AC1 23 GLY A 148 LEU A 149 ILE A 150 ASP A 172 SITE 3 AC1 23 GLN A 173 PHE A 174 CYS A 213 THR A 214 SITE 4 AC1 23 VAL A 215 THR A 216 ILE A 235 THR A 289 SITE 5 AC1 23 PRO A 306 GLY A 308 AKG A 402 HOH A 510 SITE 6 AC1 23 HOH A 548 HOH A 561 HOH A 566 SITE 1 AC2 13 LYS A 45 ARG A 60 ILE A 62 MET A 64 SITE 2 AC2 13 LYS A 78 ILE A 80 ARG A 94 ALA A 95 SITE 3 AC2 13 ARG A 122 MET A 307 GLY A 308 NAJ A 401 SITE 4 AC2 13 HOH A 536 CRYST1 61.931 61.931 151.718 90.00 90.00 90.00 P 41 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 0.016147 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016147 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006591 0.00000