HEADER LYASE 17-NOV-06 2NX9 TITLE CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE DOMAIN OF THE TITLE 2 OXALOACETATE DECARBOXYLASE NA+ PUMP FROM VIBRIO CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXALOACETATE DECARBOXYLASE 2, SUBUNIT ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CARBOXYLTRANSFERASE DOMAIN; COMPND 5 EC: 4.1.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 STRAIN: O395-N1; SOURCE 5 GENE: OADA-2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXALOACETATE DECARBOXYLASE, CARBOXYLTRANSFERASE STRUCTURE, BIOTIN KEYWDS 2 ENZYMES, ZN2+ BINDING SITE, TIM-BARREL FOLD, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR R.STUDER,P.DIMROTH REVDAT 5 30-AUG-23 2NX9 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2NX9 1 VERSN REVDAT 3 24-FEB-09 2NX9 1 VERSN REVDAT 2 13-MAR-07 2NX9 1 JRNL REVDAT 1 26-DEC-06 2NX9 0 JRNL AUTH R.STUDER,P.DAHINDEN,W.W.WANG,Y.AUCHLI,X.D.LI,P.DIMROTH JRNL TITL CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE DOMAIN OF THE JRNL TITL 2 OXALOACETATE DECARBOXYLASE NA(+) PUMP FROM VIBRIO CHOLERAE. JRNL REF J.MOL.BIOL. V. 367 547 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17270211 JRNL DOI 10.1016/J.JMB.2006.12.035 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 100388 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5272 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6774 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 360 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 539 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 31.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.13000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : 2.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.271 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7114 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9654 ; 1.441 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 906 ; 5.751 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 315 ;37.832 ;24.730 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1257 ;15.620 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;15.997 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1135 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5296 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3601 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4911 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 570 ; 0.186 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 25 ; 0.157 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.102 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4636 ; 2.084 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7231 ; 2.724 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2787 ; 4.605 ; 4.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2421 ; 5.668 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): -0.9720 17.1306 15.5066 REMARK 3 T TENSOR REMARK 3 T11: 0.0104 T22: 0.1397 REMARK 3 T33: -0.1050 T12: 0.0179 REMARK 3 T13: 0.0035 T23: 0.0693 REMARK 3 L TENSOR REMARK 3 L11: 2.0780 L22: 0.8965 REMARK 3 L33: 0.2880 L12: -0.1751 REMARK 3 L13: 0.1995 L23: -0.3755 REMARK 3 S TENSOR REMARK 3 S11: -0.0667 S12: -0.4841 S13: -0.1388 REMARK 3 S21: -0.0048 S22: 0.0145 S23: -0.0310 REMARK 3 S31: -0.0475 S32: 0.0260 S33: 0.0522 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 306 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8447 -3.4590 6.2144 REMARK 3 T TENSOR REMARK 3 T11: -0.0033 T22: -0.1082 REMARK 3 T33: 0.2760 T12: 0.0111 REMARK 3 T13: 0.0529 T23: 0.1292 REMARK 3 L TENSOR REMARK 3 L11: 2.7973 L22: 0.6800 REMARK 3 L33: 0.7474 L12: -0.4517 REMARK 3 L13: 0.4620 L23: -0.2704 REMARK 3 S TENSOR REMARK 3 S11: -0.0325 S12: -0.0405 S13: -0.9181 REMARK 3 S21: -0.4138 S22: 0.0019 S23: -0.0692 REMARK 3 S31: 0.0875 S32: 0.0886 S33: 0.0306 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 306 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8820 42.3348 -10.1051 REMARK 3 T TENSOR REMARK 3 T11: 0.0175 T22: -0.0134 REMARK 3 T33: 0.1035 T12: -0.0010 REMARK 3 T13: -0.0435 T23: 0.1095 REMARK 3 L TENSOR REMARK 3 L11: 2.1488 L22: 0.7316 REMARK 3 L33: 0.8426 L12: 0.0286 REMARK 3 L13: 0.0804 L23: -0.3620 REMARK 3 S TENSOR REMARK 3 S11: -0.0674 S12: 0.2027 S13: 0.6130 REMARK 3 S21: -0.0204 S22: 0.0423 S23: 0.0374 REMARK 3 S31: -0.0157 S32: 0.0171 S33: 0.0251 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 307 B 454 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4342 59.7473 -5.6965 REMARK 3 T TENSOR REMARK 3 T11: -0.0111 T22: -0.1147 REMARK 3 T33: 0.7054 T12: -0.0705 REMARK 3 T13: -0.0620 T23: 0.1215 REMARK 3 L TENSOR REMARK 3 L11: 1.9529 L22: 0.2669 REMARK 3 L33: 1.8226 L12: -0.1262 REMARK 3 L13: 0.5020 L23: 0.2336 REMARK 3 S TENSOR REMARK 3 S11: -0.1964 S12: 0.0161 S13: 1.2033 REMARK 3 S21: 0.0047 S22: 0.0507 S23: -0.1931 REMARK 3 S31: -0.2610 S32: 0.1428 S33: 0.1457 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2NX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.83301 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 7.140 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : 0.10400 REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 35.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.82 REMARK 200 R MERGE FOR SHELL (I) : 0.57800 REMARK 200 R SYM FOR SHELL (I) : 0.80900 REMARK 200 FOR SHELL : 2.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1RQH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-CACODYLATE 0.2 M (NH4)2SO4 5% REMARK 280 GLYCEROL 25% (W/V) PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K, PH 6.50 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 45.41250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.21100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.82750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.21100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.41250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.82750 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: 3410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 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 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 THR A 2 REMARK 465 GLN A 3 REMARK 465 HIS A 455 REMARK 465 ASN A 456 REMARK 465 LEU A 457 REMARK 465 GLU A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 HIS A 464 REMARK 465 MET B 1 REMARK 465 HIS B 455 REMARK 465 ASN B 456 REMARK 465 LEU B 457 REMARK 465 GLU B 458 REMARK 465 HIS B 459 REMARK 465 HIS B 460 REMARK 465 HIS B 461 REMARK 465 HIS B 462 REMARK 465 HIS B 463 REMARK 465 HIS B 464 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 16 -74.61 -145.26 REMARK 500 PHE A 23 62.15 -156.54 REMARK 500 CYS A 49 19.47 -146.80 REMARK 500 ARG A 87 48.33 -88.26 REMARK 500 LEU A 91 -117.60 54.01 REMARK 500 ASP A 115 -61.32 -102.46 REMARK 500 THR A 240 -115.04 45.65 REMARK 500 ASP A 259 108.50 -23.46 REMARK 500 ALA A 298 19.58 -141.79 REMARK 500 ASN A 316 -168.35 52.06 REMARK 500 TYR A 362 35.06 71.01 REMARK 500 ALA A 394 73.41 13.41 REMARK 500 ASP A 444 -122.90 51.76 REMARK 500 ARG B 16 -77.82 -142.42 REMARK 500 CYS B 49 13.06 -141.95 REMARK 500 ARG B 87 49.07 -81.40 REMARK 500 LEU B 91 -122.81 38.36 REMARK 500 ILE B 234 131.17 -37.26 REMARK 500 THR B 240 -121.62 38.31 REMARK 500 ASP B 259 111.09 -28.04 REMARK 500 ALA B 298 15.76 -158.05 REMARK 500 GLN B 315 -64.07 -90.56 REMARK 500 PRO B 383 128.54 -38.72 REMARK 500 GLU B 387 65.81 -109.87 REMARK 500 ALA B 394 -38.77 179.61 REMARK 500 ASP B 444 -124.56 49.60 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 17 OD2 REMARK 620 2 HIS A 207 NE2 86.1 REMARK 620 3 HIS A 209 NE2 90.5 87.6 REMARK 620 4 HOH A 602 O 98.6 93.9 170.9 REMARK 620 5 HOH A 695 O 87.9 172.1 87.3 92.1 REMARK 620 6 HOH A 696 O 170.3 103.2 92.8 78.1 83.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 17 OD2 REMARK 620 2 HIS B 207 NE2 88.5 REMARK 620 3 HIS B 209 NE2 97.6 91.5 REMARK 620 4 HOH B 624 O 82.4 87.1 178.7 REMARK 620 5 HOH B 678 O 159.4 88.6 102.9 77.1 REMARK 620 6 HOH B 811 O 82.2 170.4 87.1 94.3 101.0 REMARK 620 N 1 2 3 4 5 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RQH RELATED DB: PDB REMARK 900 PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO REMARK 900 PYRUVIC ACID DBREF 2NX9 A 1 456 UNP Q6A1F6 Q6A1F6_VIBCH 1 456 DBREF 2NX9 B 1 456 UNP Q6A1F6 Q6A1F6_VIBCH 1 456 SEQADV 2NX9 LEU A 457 UNP Q6A1F6 CLONING ARTIFACT SEQADV 2NX9 GLU A 458 UNP Q6A1F6 CLONING ARTIFACT SEQADV 2NX9 HIS A 459 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS A 460 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS A 461 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS A 462 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS A 463 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS A 464 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 LEU B 457 UNP Q6A1F6 CLONING ARTIFACT SEQADV 2NX9 GLU B 458 UNP Q6A1F6 CLONING ARTIFACT SEQADV 2NX9 HIS B 459 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS B 460 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS B 461 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS B 462 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS B 463 UNP Q6A1F6 EXPRESSION TAG SEQADV 2NX9 HIS B 464 UNP Q6A1F6 EXPRESSION TAG SEQRES 1 A 464 MET THR GLN ALA ILE LYS ARG VAL GLY VAL THR ASP VAL SEQRES 2 A 464 VAL LEU ARG ASP ALA HIS GLN SER LEU PHE ALA THR ARG SEQRES 3 A 464 LEU ARG ILE ASP ASP MET LEU PRO ILE ALA GLN GLN LEU SEQRES 4 A 464 ASP GLN ILE GLY TYR TRP SER LEU GLU CYS TRP GLY GLY SEQRES 5 A 464 ALA THR PHE ASP SER CYS ILE ARG PHE LEU GLY GLU ASP SEQRES 6 A 464 PRO TRP GLN ARG LEU ARG LEU LEU LYS GLN ALA MET PRO SEQRES 7 A 464 ASN THR PRO LEU GLN MET LEU LEU ARG GLY GLN ASN LEU SEQRES 8 A 464 LEU GLY TYR ARG HIS TYR ALA ASP ASP VAL VAL ASP THR SEQRES 9 A 464 PHE VAL GLU ARG ALA VAL LYS ASN GLY MET ASP VAL PHE SEQRES 10 A 464 ARG VAL PHE ASP ALA MET ASN ASP VAL ARG ASN MET GLN SEQRES 11 A 464 GLN ALA LEU GLN ALA VAL LYS LYS MET GLY ALA HIS ALA SEQRES 12 A 464 GLN GLY THR LEU CYS TYR THR THR SER PRO VAL HIS ASN SEQRES 13 A 464 LEU GLN THR TRP VAL ASP VAL ALA GLN GLN LEU ALA GLU SEQRES 14 A 464 LEU GLY VAL ASP SER ILE ALA LEU LYS ASP MET ALA GLY SEQRES 15 A 464 ILE LEU THR PRO TYR ALA ALA GLU GLU LEU VAL SER THR SEQRES 16 A 464 LEU LYS LYS GLN VAL ASP VAL GLU LEU HIS LEU HIS CYS SEQRES 17 A 464 HIS SER THR ALA GLY LEU ALA ASP MET THR LEU LEU LYS SEQRES 18 A 464 ALA ILE GLU ALA GLY VAL ASP ARG VAL ASP THR ALA ILE SEQRES 19 A 464 SER SER MET SER GLY THR TYR GLY HIS PRO ALA THR GLU SEQRES 20 A 464 SER LEU VAL ALA THR LEU GLN GLY THR GLY TYR ASP THR SEQRES 21 A 464 GLY LEU ASP ILE ALA LYS LEU GLU GLN ILE ALA ALA TYR SEQRES 22 A 464 PHE ARG ASP VAL ARG LYS LYS TYR HIS ALA PHE GLU GLY SEQRES 23 A 464 MET MET LYS GLY SER ASP ALA ARG ILE LEU VAL ALA GLN SEQRES 24 A 464 VAL PRO GLY GLY MET LEU THR ASN MET GLU SER GLN LEU SEQRES 25 A 464 LYS GLN GLN ASN ALA LEU ASP LYS LEU ASP LEU VAL LEU SEQRES 26 A 464 GLU GLU ILE PRO ARG VAL ARG GLU GLU LEU GLY PHE LEU SEQRES 27 A 464 PRO LEU VAL THR PRO THR SER GLN ILE VAL GLY THR GLN SEQRES 28 A 464 ALA VAL ILE ASN VAL VAL LEU GLY GLU ARG TYR LYS THR SEQRES 29 A 464 ILE THR LYS GLU THR SER GLY VAL LEU LYS GLY GLU TYR SEQRES 30 A 464 GLY LYS THR PRO ALA PRO VAL ASN THR GLU LEU GLN ALA SEQRES 31 A 464 ARG VAL LEU ALA GLY ALA GLU ALA ILE THR CYS ARG PRO SEQRES 32 A 464 ALA ASP LEU ILE ALA ALA GLU MET PRO THR LEU GLN ASP SEQRES 33 A 464 ARG VAL LEU GLN GLN ALA LYS GLU GLN HIS ILE THR LEU SEQRES 34 A 464 ALA GLU ASN ALA ILE ASP ASP VAL LEU THR ILE ALA LEU SEQRES 35 A 464 PHE ASP GLN VAL GLY TRP LYS PHE LEU ALA ASN ARG HIS SEQRES 36 A 464 ASN LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 464 MET THR GLN ALA ILE LYS ARG VAL GLY VAL THR ASP VAL SEQRES 2 B 464 VAL LEU ARG ASP ALA HIS GLN SER LEU PHE ALA THR ARG SEQRES 3 B 464 LEU ARG ILE ASP ASP MET LEU PRO ILE ALA GLN GLN LEU SEQRES 4 B 464 ASP GLN ILE GLY TYR TRP SER LEU GLU CYS TRP GLY GLY SEQRES 5 B 464 ALA THR PHE ASP SER CYS ILE ARG PHE LEU GLY GLU ASP SEQRES 6 B 464 PRO TRP GLN ARG LEU ARG LEU LEU LYS GLN ALA MET PRO SEQRES 7 B 464 ASN THR PRO LEU GLN MET LEU LEU ARG GLY GLN ASN LEU SEQRES 8 B 464 LEU GLY TYR ARG HIS TYR ALA ASP ASP VAL VAL ASP THR SEQRES 9 B 464 PHE VAL GLU ARG ALA VAL LYS ASN GLY MET ASP VAL PHE SEQRES 10 B 464 ARG VAL PHE ASP ALA MET ASN ASP VAL ARG ASN MET GLN SEQRES 11 B 464 GLN ALA LEU GLN ALA VAL LYS LYS MET GLY ALA HIS ALA SEQRES 12 B 464 GLN GLY THR LEU CYS TYR THR THR SER PRO VAL HIS ASN SEQRES 13 B 464 LEU GLN THR TRP VAL ASP VAL ALA GLN GLN LEU ALA GLU SEQRES 14 B 464 LEU GLY VAL ASP SER ILE ALA LEU LYS ASP MET ALA GLY SEQRES 15 B 464 ILE LEU THR PRO TYR ALA ALA GLU GLU LEU VAL SER THR SEQRES 16 B 464 LEU LYS LYS GLN VAL ASP VAL GLU LEU HIS LEU HIS CYS SEQRES 17 B 464 HIS SER THR ALA GLY LEU ALA ASP MET THR LEU LEU LYS SEQRES 18 B 464 ALA ILE GLU ALA GLY VAL ASP ARG VAL ASP THR ALA ILE SEQRES 19 B 464 SER SER MET SER GLY THR TYR GLY HIS PRO ALA THR GLU SEQRES 20 B 464 SER LEU VAL ALA THR LEU GLN GLY THR GLY TYR ASP THR SEQRES 21 B 464 GLY LEU ASP ILE ALA LYS LEU GLU GLN ILE ALA ALA TYR SEQRES 22 B 464 PHE ARG ASP VAL ARG LYS LYS TYR HIS ALA PHE GLU GLY SEQRES 23 B 464 MET MET LYS GLY SER ASP ALA ARG ILE LEU VAL ALA GLN SEQRES 24 B 464 VAL PRO GLY GLY MET LEU THR ASN MET GLU SER GLN LEU SEQRES 25 B 464 LYS GLN GLN ASN ALA LEU ASP LYS LEU ASP LEU VAL LEU SEQRES 26 B 464 GLU GLU ILE PRO ARG VAL ARG GLU GLU LEU GLY PHE LEU SEQRES 27 B 464 PRO LEU VAL THR PRO THR SER GLN ILE VAL GLY THR GLN SEQRES 28 B 464 ALA VAL ILE ASN VAL VAL LEU GLY GLU ARG TYR LYS THR SEQRES 29 B 464 ILE THR LYS GLU THR SER GLY VAL LEU LYS GLY GLU TYR SEQRES 30 B 464 GLY LYS THR PRO ALA PRO VAL ASN THR GLU LEU GLN ALA SEQRES 31 B 464 ARG VAL LEU ALA GLY ALA GLU ALA ILE THR CYS ARG PRO SEQRES 32 B 464 ALA ASP LEU ILE ALA ALA GLU MET PRO THR LEU GLN ASP SEQRES 33 B 464 ARG VAL LEU GLN GLN ALA LYS GLU GLN HIS ILE THR LEU SEQRES 34 B 464 ALA GLU ASN ALA ILE ASP ASP VAL LEU THR ILE ALA LEU SEQRES 35 B 464 PHE ASP GLN VAL GLY TRP LYS PHE LEU ALA ASN ARG HIS SEQRES 36 B 464 ASN LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 601 1 HET ZN B 602 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *539(H2 O) HELIX 1 1 ARG A 16 PHE A 23 1 8 HELIX 2 2 ARG A 28 PRO A 34 5 7 HELIX 3 3 ILE A 35 GLN A 41 1 7 HELIX 4 4 ALA A 53 PHE A 61 1 9 HELIX 5 5 ASP A 65 MET A 77 1 13 HELIX 6 6 ARG A 87 LEU A 91 5 5 HELIX 7 7 ALA A 98 ASN A 112 1 15 HELIX 8 8 VAL A 126 MET A 139 1 14 HELIX 9 9 ASN A 156 LEU A 170 1 15 HELIX 10 10 THR A 185 VAL A 200 1 16 HELIX 11 11 LEU A 214 ALA A 225 1 12 HELIX 12 12 ILE A 234 SER A 238 5 5 HELIX 13 13 ALA A 245 GLN A 254 1 10 HELIX 14 14 ASP A 263 TYR A 281 1 19 HELIX 15 15 HIS A 282 GLU A 285 5 4 HELIX 16 16 ALA A 293 GLN A 299 1 7 HELIX 17 17 PRO A 301 GLN A 314 1 14 HELIX 18 18 ALA A 317 ASP A 319 5 3 HELIX 19 19 LYS A 320 LEU A 335 1 16 HELIX 20 20 PRO A 343 LEU A 358 1 16 HELIX 21 21 THR A 366 LYS A 374 1 9 HELIX 22 22 ASN A 385 ALA A 394 1 10 HELIX 23 23 ARG A 402 LEU A 406 5 5 HELIX 24 24 GLU A 410 GLN A 425 1 16 HELIX 25 25 ASN A 432 ARG A 454 1 23 HELIX 26 26 ARG B 16 PHE B 23 1 8 HELIX 27 27 ARG B 28 LEU B 33 1 6 HELIX 28 28 ILE B 35 GLN B 41 1 7 HELIX 29 29 ALA B 53 PHE B 61 1 9 HELIX 30 30 ASP B 65 MET B 77 1 13 HELIX 31 31 ARG B 87 LEU B 91 5 5 HELIX 32 32 ALA B 98 GLY B 113 1 16 HELIX 33 33 ASP B 125 MET B 139 1 15 HELIX 34 34 ASN B 156 LEU B 170 1 15 HELIX 35 35 THR B 185 VAL B 200 1 16 HELIX 36 36 LEU B 214 ALA B 225 1 12 HELIX 37 37 ILE B 234 SER B 238 5 5 HELIX 38 38 ALA B 245 GLN B 254 1 10 HELIX 39 39 ASP B 263 LYS B 280 1 18 HELIX 40 40 TYR B 281 GLU B 285 5 5 HELIX 41 41 ALA B 293 GLN B 299 1 7 HELIX 42 42 PRO B 301 GLN B 314 1 14 HELIX 43 43 ALA B 317 ASP B 319 5 3 HELIX 44 44 LYS B 320 LEU B 335 1 16 HELIX 45 45 PRO B 343 GLY B 359 1 17 HELIX 46 46 THR B 366 LYS B 374 1 9 HELIX 47 47 LEU B 388 ALA B 394 1 7 HELIX 48 48 ARG B 402 LEU B 406 5 5 HELIX 49 49 GLU B 410 GLN B 425 1 16 HELIX 50 50 ALA B 433 ASP B 444 1 12 HELIX 51 51 ASP B 444 ARG B 454 1 11 SHEET 1 A 9 GLY A 9 ASP A 12 0 SHEET 2 A 9 SER A 46 GLY A 51 1 O GLU A 48 N ASP A 12 SHEET 3 A 9 LEU A 82 LEU A 86 1 O GLN A 83 N LEU A 47 SHEET 4 A 9 VAL A 116 VAL A 119 1 O ARG A 118 N LEU A 86 SHEET 5 A 9 HIS A 142 CYS A 148 1 O GLN A 144 N PHE A 117 SHEET 6 A 9 SER A 174 ASP A 179 1 O ALA A 176 N GLY A 145 SHEET 7 A 9 LEU A 204 CYS A 208 1 O HIS A 207 N ASP A 179 SHEET 8 A 9 ARG A 229 THR A 232 1 O ARG A 229 N LEU A 206 SHEET 9 A 9 GLY A 9 ASP A 12 1 N THR A 11 O VAL A 230 SHEET 1 B 9 GLY B 9 ASP B 12 0 SHEET 2 B 9 SER B 46 GLY B 51 1 O GLU B 48 N ASP B 12 SHEET 3 B 9 LEU B 82 LEU B 86 1 O GLN B 83 N CYS B 49 SHEET 4 B 9 VAL B 116 VAL B 119 1 O ARG B 118 N LEU B 86 SHEET 5 B 9 HIS B 142 CYS B 148 1 O HIS B 142 N PHE B 117 SHEET 6 B 9 SER B 174 ASP B 179 1 O ALA B 176 N GLY B 145 SHEET 7 B 9 LEU B 204 CYS B 208 1 O HIS B 207 N ASP B 179 SHEET 8 B 9 ARG B 229 THR B 232 1 O ARG B 229 N LEU B 206 SHEET 9 B 9 GLY B 9 ASP B 12 1 N THR B 11 O THR B 232 LINK OD2 ASP A 17 ZN ZN A 601 1555 1555 2.20 LINK NE2 HIS A 207 ZN ZN A 601 1555 1555 2.32 LINK NE2 HIS A 209 ZN ZN A 601 1555 1555 2.19 LINK ZN ZN A 601 O HOH A 602 1555 1555 2.29 LINK ZN ZN A 601 O HOH A 695 1555 1555 2.15 LINK ZN ZN A 601 O HOH A 696 1555 1555 2.12 LINK OD2 ASP B 17 ZN ZN B 602 1555 1555 2.05 LINK NE2 HIS B 207 ZN ZN B 602 1555 1555 2.31 LINK NE2 HIS B 209 ZN ZN B 602 1555 1555 2.14 LINK ZN ZN B 602 O HOH B 624 1555 1555 2.22 LINK ZN ZN B 602 O HOH B 678 1555 1555 2.18 LINK ZN ZN B 602 O HOH B 811 1555 1555 2.23 CISPEP 1 THR A 342 PRO A 343 0 10.34 CISPEP 2 ALA A 394 GLY A 395 0 -2.34 CISPEP 3 GLN B 315 ASN B 316 0 -5.61 CISPEP 4 ASN B 316 ALA B 317 0 13.20 CISPEP 5 THR B 342 PRO B 343 0 4.57 CISPEP 6 THR B 386 GLU B 387 0 3.35 CISPEP 7 ALA B 394 GLY B 395 0 6.05 SITE 1 AC1 6 ASP A 17 HIS A 207 HIS A 209 HOH A 602 SITE 2 AC1 6 HOH A 695 HOH A 696 SITE 1 AC2 6 ASP B 17 HIS B 207 HIS B 209 HOH B 624 SITE 2 AC2 6 HOH B 678 HOH B 811 CRYST1 90.825 91.655 116.422 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 0.011010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008589 0.00000