10 20 30 40 50 60 70 80 2E1Y - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 04-NOV-06 2E1Y
TITLE CRYSTAL STRUCTURE OF PROPIONATE KINASE (TDCD) FROM TITLE 2 SALMONELLA TYPHIMURIUM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPIONATE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.2.15; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 STRAIN: IFO 12529; SOURCE 5 GENE: TDCD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET C
KEYWDS PROPIONATE KINASE, TDCD, NATIVE, ACETATE KINASE, NUCLEOTIDE, KEYWDS 2 AP4A, ADP, ATP, AMPPNP, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.K.SIMANSHU,H.S.SAVITHRI,M.R.N.MURTHY
REVDAT 3 24-FEB-09 2E1Y 1 VERSN REVDAT 2 04-NOV-08 2E1Y 1 JRNL REVDAT 1 18-SEP-07 2E1Y 0
JRNL AUTH D.K.SIMANSHU,H.S.SAVITHRI,M.R.N.MURTHY JRNL TITL CRYSTAL STRUCTURES OF SALMONELLA TYPHIMURIUM JRNL TITL 2 PROPIONATE KINASE AND ITS COMPLEX WITH AP4A: JRNL TITL 3 EVIDENCE FOR A NOVEL AP4A SYNTHETIC ACTIVITY. JRNL REF PROTEINS V. 70 1379 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 17894350 JRNL DOI 10.1002/PROT.21626
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.K.SIMANSHU,H.S.SAVITHRI,M.R.MURTHY REMARK 1 TITL CRYSTAL STRUCTURES OF ADP AND AMPPNP-BOUND REMARK 1 TITL 2 PROPIONATE KINASE (TDCD) FROM SALMONELLA REMARK 1 TITL 3 TYPHIMURIUM: COMPARISON WITH MEMBERS OF ACETATE REMARK 1 TITL 4 AND SUGAR KINASE/HEAT SHOCK COGNATE 70/ACTIN REMARK 1 TITL 5 SUPERFAMILY REMARK 1 REF J.MOL.BIOL. V. 352 876 2005 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 16139298 REMARK 1 DOI 10.1016/J.JMB.2005.07.069 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.K.SIMANSHU,M.R.MURTHY REMARK 1 TITL CLONING, EXPRESSION, PURIFICATION, CRYSTALLIZATION REMARK 1 TITL 2 AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS OF REMARK 1 TITL 3 PROPIONATE KINASE (TDCD) FROM SALMONELLA REMARK 1 TITL 4 TYPHIMURIUM REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 61 52 2005 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 16508089 REMARK 1 DOI 10.1107/S1744309104026429
REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 13415 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 706 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 768 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2944 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.10000 REMARK 3 B22 (A**2) : 2.10000 REMARK 3 B33 (A**2) : -3.15000 REMARK 3 B12 (A**2) : 1.05000 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): 0.847 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.324 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.248 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.101 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2998 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1939 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4075 ; 0.932 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4726 ; 0.809 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 5.554 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;32.526 ;23.438 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;13.691 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.877 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 476 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3422 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 609 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 696 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2065 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1492 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1593 ; 0.081 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 109 ; 0.142 ; 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): 20 ; 0.111 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.190 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.116 ; 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): 1991 ; 0.387 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 812 ; 0.041 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3101 ; 0.697 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1109 ; 0.685 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 973 ; 1.199 ; 4.500 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 : NULL 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2E1Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-06. REMARK 100 THE RCSB ID CODE IS RCSB026124.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14818 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 33.560 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: DIFFERENCE FOURIER REMARK 200 STARTING MODEL: PDB ENTRY 1X3M REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 BIS-TRIS PH 6.5, 30% (V/V) REMARK 280 PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), MICROBATCH METHOD, REMARK 280 TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.17767 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.35533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.35533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.17767 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: 6310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.53300
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 494 LIES ON A SPECIAL POSITION.
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 -12 REMARK 465 ARG A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 GLY A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 398 REMARK 465 VAL A 399 REMARK 465 GLU A 400 REMARK 465 PHE A 401 REMARK 465 ALA A 402
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 PHE A 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 39 CG OD1 ND2 REMARK 470 THR A 40 OG1 CG2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 ASN A 42 CG OD1 ND2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 ILE A 53 CG1 CG2 CD1 REMARK 470 ASN A 54 CG OD1 ND2 REMARK 470 LEU A 55 CG CD1 CD2 REMARK 470 HIS A 57 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 58 OG REMARK 470 LEU A 64 CG CD1 CD2 REMARK 470 LYS A 65 CG CD CE NZ REMARK 470 PHE A 69 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 ASP A 78 CG OD1 OD2 REMARK 470 LEU A 117 CG CD1 CD2 REMARK 470 SER A 166 OG REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 LYS A 284 CG CD CE NZ REMARK 470 LYS A 355 CG CD CE NZ
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 ILE A 34 119.62 -167.05 REMARK 500 ASN A 39 -21.71 79.14 REMARK 500 LYS A 51 82.16 -179.69 REMARK 500 PRO A 52 90.87 -40.48 REMARK 500 LEU A 55 35.86 -145.68 REMARK 500 ARG A 74 31.53 -99.47 REMARK 500 ALA A 115 70.08 -154.05 REMARK 500 ASN A 206 -81.56 -19.65 REMARK 500 MET A 233 -166.25 -128.35 REMARK 500 SER A 267 -164.30 -107.55 REMARK 500 LEU A 275 -62.57 -151.19 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 442 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH A 470 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A 490 DISTANCE = 7.82 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X3M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP BOUND PROPIONATE KINASE (TDCD) REMARK 900 FROM SALMONELLA TYPHIMURIUM REMARK 900 RELATED ID: 1X3N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPPNP BOUND PROPIONATE KINASE (TDCD) REMARK 900 FROM SALMONELLA TYPHIMURIUM REMARK 900 RELATED ID: 2E1Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE REMARK 900 KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE REMARK 900 (AP4A) OBTAINED AFTER CO-CRYSTALLIZATION WITH ATP REMARK 900 RELATED ID: 2E20 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE REMARK 900 KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE REMARK 900 (AP4A)
DBREF 2E1Y A 2 402 UNP O06961 TDCD_SALTY 2 402
SEQADV 2E1Y MET A -12 UNP O06961 EXPRESSION TAG SEQADV 2E1Y ARG A -11 UNP O06961 EXPRESSION TAG SEQADV 2E1Y GLY A -10 UNP O06961 EXPRESSION TAG SEQADV 2E1Y SER A -9 UNP O06961 EXPRESSION TAG SEQADV 2E1Y HIS A -8 UNP O06961 EXPRESSION TAG SEQADV 2E1Y HIS A -7 UNP O06961 EXPRESSION TAG SEQADV 2E1Y HIS A -6 UNP O06961 EXPRESSION TAG SEQADV 2E1Y HIS A -5 UNP O06961 EXPRESSION TAG SEQADV 2E1Y HIS A -4 UNP O06961 EXPRESSION TAG SEQADV 2E1Y HIS A -3 UNP O06961 EXPRESSION TAG SEQADV 2E1Y GLY A -2 UNP O06961 EXPRESSION TAG SEQADV 2E1Y MET A -1 UNP O06961 EXPRESSION TAG SEQADV 2E1Y ALA A 0 UNP O06961 EXPRESSION TAG SEQADV 2E1Y SER A 1 UNP O06961 EXPRESSION TAG
SEQRES 1 A 415 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 415 SER ASN GLU PHE PRO VAL VAL LEU VAL ILE ASN CYS GLY SEQRES 3 A 415 SER SER SER ILE LYS PHE SER VAL LEU ASP VAL ALA THR SEQRES 4 A 415 CYS ASP VAL LEU MET ALA GLY ILE ALA ASP GLY MET ASN SEQRES 5 A 415 THR GLU ASN ALA PHE LEU SER ILE ASN GLY ASP LYS PRO SEQRES 6 A 415 ILE ASN LEU ALA HIS SER ASN TYR GLU ASP ALA LEU LYS SEQRES 7 A 415 ALA ILE ALA PHE GLU LEU GLU LYS ARG ASP LEU THR ASP SEQRES 8 A 415 SER VAL ALA LEU ILE GLY HIS ARG ILE ALA HIS GLY GLY SEQRES 9 A 415 GLU LEU PHE THR GLN SER VAL ILE ILE THR ASP GLU ILE SEQRES 10 A 415 ILE ASP ASN ILE ARG ARG VAL SER PRO LEU ALA PRO LEU SEQRES 11 A 415 HIS ASN TYR ALA ASN LEU SER GLY ILE ASP ALA ALA ARG SEQRES 12 A 415 HIS LEU PHE PRO ALA VAL ARG GLN VAL ALA VAL PHE ASP SEQRES 13 A 415 THR SER PHE HIS GLN THR LEU ALA PRO GLU ALA TYR LEU SEQRES 14 A 415 TYR GLY LEU PRO TRP GLU TYR PHE SER SER LEU GLY VAL SEQRES 15 A 415 ARG ARG TYR GLY PHE HIS GLY THR SER HIS ARG TYR VAL SEQRES 16 A 415 SER ARG ARG ALA TYR GLU LEU LEU ASP LEU ASP GLU LYS SEQRES 17 A 415 ASP SER GLY LEU ILE VAL ALA HIS LEU GLY ASN GLY ALA SEQRES 18 A 415 SER ILE CYS ALA VAL ARG ASN GLY GLN SER VAL ASP THR SEQRES 19 A 415 SER MET GLY MET THR PRO LEU GLU GLY LEU MET MET GLY SEQRES 20 A 415 THR ARG SER GLY ASP VAL ASP PHE GLY ALA MET ALA TRP SEQRES 21 A 415 ILE ALA LYS GLU THR GLY GLN THR LEU SER ASP LEU GLU SEQRES 22 A 415 ARG VAL VAL ASN LYS GLU SER GLY LEU LEU GLY ILE SER SEQRES 23 A 415 GLY LEU SER SER ASP LEU ARG VAL LEU GLU LYS ALA TRP SEQRES 24 A 415 HIS GLU GLY HIS GLU ARG ALA ARG LEU ALA ILE LYS THR SEQRES 25 A 415 PHE VAL HIS ARG ILE ALA ARG HIS ILE ALA GLY HIS ALA SEQRES 26 A 415 ALA SER LEU HIS ARG LEU ASP GLY ILE ILE PHE THR GLY SEQRES 27 A 415 GLY ILE GLY GLU ASN SER VAL LEU ILE ARG GLN LEU VAL SEQRES 28 A 415 ILE GLU HIS LEU GLY VAL LEU GLY LEU THR LEU ASP VAL SEQRES 29 A 415 GLU MET ASN LYS GLN PRO ASN SER HIS GLY GLU ARG ILE SEQRES 30 A 415 ILE SER ALA ASN PRO SER GLN VAL ILE CYS ALA VAL ILE SEQRES 31 A 415 PRO THR ASN GLU GLU LYS MET ILE ALA LEU ASP ALA ILE SEQRES 32 A 415 HIS LEU GLY ASN VAL LYS ALA PRO VAL GLU PHE ALA
FORMUL 2 HOH *104(H2 O)
HELIX 1 1 ASN A 59 ARG A 74 1 16 HELIX 2 2 THR A 101 SER A 112 1 12 HELIX 3 3 ALA A 115 PHE A 133 1 19 HELIX 4 4 THR A 144 LEU A 150 5 7 HELIX 5 5 ALA A 151 LEU A 156 1 6 HELIX 6 6 PRO A 160 SER A 166 1 7 HELIX 7 7 HIS A 175 ASP A 191 1 17 HELIX 8 8 ASP A 193 ASP A 196 5 4 HELIX 9 9 ASP A 241 GLY A 253 1 13 HELIX 10 10 THR A 255 GLU A 266 1 12 HELIX 11 11 SER A 267 GLY A 274 1 8 HELIX 12 12 ASP A 278 GLU A 288 1 11 HELIX 13 13 HIS A 290 ALA A 312 1 23 HELIX 14 14 ALA A 313 LEU A 315 5 3 HELIX 15 15 GLY A 325 SER A 331 1 7 HELIX 16 16 SER A 331 HIS A 341 1 11 HELIX 17 17 LEU A 342 GLY A 346 5 5 HELIX 18 18 ASP A 350 GLN A 356 1 7 HELIX 19 19 PRO A 357 GLY A 361 5 5 HELIX 20 20 ASN A 380 ASN A 394 1 15
SHEET 1 A 7 PHE A 44 ILE A 47 0 SHEET 2 A 7 VAL A 29 ASP A 36 -1 N ILE A 34 O SER A 46 SHEET 3 A 7 LYS A 18 ASP A 23 -1 N VAL A 21 O LEU A 30 SHEET 4 A 7 VAL A 6 ASN A 11 -1 N ASN A 11 O LYS A 18 SHEET 5 A 7 VAL A 80 ILE A 87 1 O LEU A 82 N LEU A 8 SHEET 6 A 7 ARG A 137 PHE A 142 1 O VAL A 141 N HIS A 85 SHEET 7 A 7 VAL A 98 ILE A 99 -1 N VAL A 98 O ALA A 140 SHEET 1 B 6 GLN A 217 THR A 221 0 SHEET 2 B 6 ALA A 208 ARG A 214 -1 N ARG A 214 O GLN A 217 SHEET 3 B 6 GLY A 198 LEU A 204 -1 N LEU A 199 O VAL A 213 SHEET 4 B 6 GLY A 320 THR A 324 1 O THR A 324 N LEU A 204 SHEET 5 B 6 ILE A 373 VAL A 376 1 O ALA A 375 N PHE A 323 SHEET 6 B 6 ARG A 363 ILE A 364 -1 N ARG A 363 O VAL A 376
CRYST1 110.811 110.811 66.533 90.00 90.00 120.00 P 31 2 1 6
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 0.009024 0.005210 0.000000 0.00000
SCALE2 0.000000 0.010420 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015030 0.00000