10 20 30 40 50 60 70 80 1LWB - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 31-MAY-02 1LWB
TITLE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2 AT ATOMIC TITLE 2 RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOLIPASE A2; COMPND 5 EC: 3.1.1.4; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VIOLACEORUBER; SOURCE 3 ORGANISM_TAXID: 1935; SOURCE 4 EXPRESSION_SYSTEM: STREPTOMYCES LIVIDANS TK24; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 457428; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TK24; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PIJ680
KEYWDS PHOSPHOLIPASE A2, ATOMIC RESOLUTION, INTERNAL MOTION, KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.MATOBA,M.SUGIYAMA
REVDAT 2 24-FEB-09 1LWB 1 VERSN REVDAT 1 10-JUN-03 1LWB 0
JRNL AUTH Y.MATOBA,M.SUGIYAMA JRNL TITL ATOMIC RESOLUTION STRUCTURE OF PROKARYOTIC JRNL TITL 2 PHOSPHOLIPASE A2: ANALYSIS OF INTERNAL MOTION AND JRNL TITL 3 IMPLICATION FOR A CATALYTIC MECHANISM. JRNL REF PROTEINS: V. 51 453 2003 JRNL REF 2 STRUCT.,FUNCT.,GENET. JRNL REFN ISSN 0887-3585 JRNL PMID 12696056 JRNL DOI 10.1002/PROT.10360
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.MATOBA,Y.KATSUBE,M.SUGIYAMA REMARK 1 TITL THE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE REMARK 1 TITL 2 A2 REMARK 1 REF J.BIOL.CHEM. V. 277 20059 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M200263200 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.SUGIYAMA,K.OHTANI,M.IZUHARA,T.KOIKE,K.SUZUKI, REMARK 1 AUTH 2 S.IMAMURA,H.MISAKI REMARK 1 TITL A NOVEL PROKARYOTIC PHOSPHOLIPASE A2. REMARK 1 TITL 2 CHARACTERIZATON, GENE CLONING AND SOLUTION REMARK 1 TITL 3 STRUCTURE REMARK 1 REF J.BIOL.CHEM. V. 277 20051 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M200264200
REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.103 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.097 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3423 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 37649 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.090 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.087 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.128 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2934 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31531 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1852 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1120.70 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 844.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 34 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10812 REMARK 3 NUMBER OF RESTRAINTS : 13414 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.104 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.128 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.035 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.010 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.132 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC TEMPERATURE FACTOR WAS REMARK 3 INTRODUCED.
REMARK 4 REMARK 4 1LWB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUN-02. REMARK 100 THE RCSB ID CODE IS RCSB016341.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1997 REMARK 200 TEMPERATURE (KELVIN) : 297 REMARK 200 PH : 6 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) : 0.71073 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45532 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.923 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 67.5 REMARK 200 DATA REDUNDANCY : 2.650 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 22.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1FAZ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 17.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, LITHIUM SULFATE, SODIUM REMARK 280 CACODYLATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.74750 REMARK 290 SMTRY3 2 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 300 REMARK: THIS ENZYME IS A MONOMERIC PROTEIN IN SOLUTION.
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: MONOMERIC 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 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 ASP A 50 CB - CG - OD1 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 50 CB - CG - OD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 TYR A 68 CB - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TYR A 68 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 85 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A 99 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR A 99 CG - CD2 - CE2 ANGL. DEV. = 5.0 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 LEU A 44 -138.43 56.58 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FAZ RELATED DB: PDB REMARK 900 1FAZ CONTAINS CRYSTAL STRUCTURE OF CALCIUM-FREE FORM AT 1.4 REMARK 900 A RESOLUTION REMARK 900 RELATED ID: 1KP4 RELATED DB: PDB REMARK 900 1KP4 CONTAINS CRYSTAL STRUCTURE OF CALCIUM-BOUND FORM AT REMARK 900 1.6 A RESOLUTION REMARK 900 RELATED ID: 1IT4 RELATED DB: PDB REMARK 900 1IT4 CONTAINS SOLUTION STRUCTURE OF CALCIUM-BOUND FORM REMARK 900 RELATED ID: 1IT5 RELATED DB: PDB REMARK 900 1IT5 CONTAINS SOLUTION STRUCTURE OF CALCIUM-FREE FORM
DBREF 1LWB A 1 122 UNP Q9Z4W2 Q9Z4W2_STRCO 30 151
SEQRES 1 A 122 ALA PRO ALA ASP LYS PRO GLN VAL LEU ALA SER PHE THR SEQRES 2 A 122 GLN THR SER ALA SER SER GLN ASN ALA TRP LEU ALA ALA SEQRES 3 A 122 ASN ARG ASN GLN SER ALA TRP ALA ALA TYR GLU PHE ASP SEQRES 4 A 122 TRP SER THR ASP LEU CYS THR GLN ALA PRO ASP ASN PRO SEQRES 5 A 122 PHE GLY PHE PRO PHE ASN THR ALA CYS ALA ARG HIS ASP SEQRES 6 A 122 PHE GLY TYR ARG ASN TYR LYS ALA ALA GLY SER PHE ASP SEQRES 7 A 122 ALA ASN LYS SER ARG ILE ASP SER ALA PHE TYR GLU ASP SEQRES 8 A 122 MET LYS ARG VAL CYS THR GLY TYR THR GLY GLU LYS ASN SEQRES 9 A 122 THR ALA CYS ASN SER THR ALA TRP THR TYR TYR GLN ALA SEQRES 10 A 122 VAL LYS ILE PHE GLY
FORMUL 2 HOH *177(H2 O)
HELIX 1 1 ASP A 4 PHE A 12 1 9 HELIX 2 2 SER A 16 ASN A 29 1 14 HELIX 3 3 GLN A 30 GLU A 37 5 8 HELIX 4 4 PHE A 57 GLY A 75 1 19 HELIX 5 5 SER A 76 THR A 97 1 22 HELIX 6 6 THR A 100 ILE A 120 1 21
SSBOND 1 CYS A 45 CYS A 61 1555 1555 2.02 SSBOND 2 CYS A 96 CYS A 107 1555 1555 2.02
CRYST1 29.340 57.495 31.807 90.00 111.07 90.00 P 1 21 1 2
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 0.034083 0.000000 0.013128 0.00000
SCALE2 0.000000 0.017393 0.000000 0.00000
SCALE3 0.000000 0.000000 0.033691 0.00000