HEADER FATTY ACID METABOLISM 16-APR-01 1HBK TITLE ACYL-COA BINDING PROTEIN FROM PLASMODIUM FALCIPARUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-COA BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACBP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS FATTY ACID METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR D.M.F.VAN AALTEN REVDAT 8 08-MAY-24 1HBK 1 REMARK LINK REVDAT 7 09-OCT-19 1HBK 1 REMARK REVDAT 6 24-JUL-19 1HBK 1 REMARK REVDAT 5 31-JAN-18 1HBK 1 AUTHOR JRNL REMARK REVDAT 4 24-FEB-09 1HBK 1 VERSN REVDAT 3 27-MAR-07 1HBK 1 JRNL REMARK REVDAT 2 13-JUN-06 1HBK 1 REMARK DBREF SEQRES REVDAT 1 15-MAY-01 1HBK 0 JRNL AUTH D.M.VAN AALTEN,K.G.MILNE,J.Y.ZOU,G.J.KLEYWEGT,T.BERGFORS, JRNL AUTH 2 M.A.FERGUSON,J.KNUDSEN,T.A.JONES JRNL TITL BINDING SITE DIFFERENCES REVEALED BY CRYSTAL STRUCTURES OF JRNL TITL 2 PLASMODIUM FALCIPARUM AND BOVINE ACYL-COA BINDING PROTEIN. JRNL REF J. MOL. BIOL. V. 309 181 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11491287 JRNL DOI 10.1006/JMBI.2001.4749 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 798970.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7714 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 SET) : 0.198 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.400 REMARK 3 FREE R VALUE TEST SET COUNT : 497 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1194 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.12000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.340 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 61.66 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : COA.PAR REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : COA.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-01. REMARK 100 THE DEPOSITION ID IS D_1290006106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.71000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 24.20550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.30825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.10275 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 44 CG CD CE NZ REMARK 480 LYS A 50 NZ 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 A2020 DISTANCE = 6.40 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 COA A 1089 REMARK 610 MYR A 1090 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 NI A1092 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 0 ND1 REMARK 620 2 HIS A 0 N 93.8 REMARK 620 3 HOH A2002 O 114.5 84.8 REMARK 620 4 HOH A2043 O 101.9 158.0 102.3 REMARK 620 5 HOH A2071 O 108.2 96.8 137.1 63.8 REMARK 620 6 HOH A2076 O 167.9 92.8 76.2 69.3 60.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1091 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 7 OE2 REMARK 620 2 HIS A 49 NE2 94.7 REMARK 620 3 HOH A2008 O 90.7 158.7 REMARK 620 4 HOH A2009 O 92.2 92.0 67.2 REMARK 620 5 HOH A2038 O 178.1 85.3 88.6 85.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1091 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1092 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COA A1089 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR A1090 DBREF 1HBK A 0 0 PDB 1HBK 1HBK 0 0 DBREF 1HBK A 1 88 UNP Q8IK57 Q8IK57_PLAF7 1 88 SEQRES 1 A 89 HIS MET ALA GLN VAL PHE GLU GLU CYS VAL SER PHE ILE SEQRES 2 A 89 ASN GLY LEU PRO ARG THR ILE ASN LEU PRO ASN GLU LEU SEQRES 3 A 89 LYS LEU ASP LEU TYR LYS TYR TYR LYS GLN SER THR ILE SEQRES 4 A 89 GLY ASN CYS ASN ILE LYS GLU PRO SER ALA HIS LYS TYR SEQRES 5 A 89 ILE ASP ARG LYS LYS TYR GLU ALA TRP LYS SER VAL GLU SEQRES 6 A 89 ASN LEU ASN ARG GLU ASP ALA GLN LYS ARG TYR VAL ASP SEQRES 7 A 89 ILE VAL SER GLU ILE PHE PRO TYR TRP GLN ASP HET COA A1089 31 HET MYR A1090 12 HET NI A1091 1 HET NI A1092 1 HETNAM COA COENZYME A HETNAM MYR MYRISTIC ACID HETNAM NI NICKEL (II) ION FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 MYR C14 H28 O2 FORMUL 4 NI 2(NI 2+) FORMUL 6 HOH *76(H2 O) HELIX 1 1 HIS A 0 LEU A 15 1 16 HELIX 2 2 PRO A 22 ILE A 38 1 17 HELIX 3 3 LYS A 50 VAL A 63 1 14 HELIX 4 4 ASN A 67 PHE A 83 1 17 LINK ND1 HIS A 0 NI NI A1092 1555 1555 1.98 LINK N HIS A 0 NI NI A1092 1555 1555 2.13 LINK OE2 GLU A 7 NI NI A1091 3554 1555 2.28 LINK NE2 HIS A 49 NI NI A1091 1555 1555 1.88 LINK NI NI A1091 O HOH A2008 1555 3554 1.74 LINK NI NI A1091 O HOH A2009 1555 3554 2.19 LINK NI NI A1091 O HOH A2038 1555 1555 2.24 LINK NI NI A1092 O HOH A2002 1555 1555 1.78 LINK NI NI A1092 O HOH A2043 1555 2565 2.48 LINK NI NI A1092 O HOH A2071 1555 4565 2.52 LINK NI NI A1092 O HOH A2076 1555 2565 2.31 SITE 1 AC1 5 GLU A 7 HIS A 49 HOH A2008 HOH A2009 SITE 2 AC1 5 HOH A2038 SITE 1 AC2 5 HIS A 0 HOH A2002 HOH A2043 HOH A2071 SITE 2 AC2 5 HOH A2076 SITE 1 AC3 16 ILE A 12 ASN A 13 TYR A 30 TYR A 33 SITE 2 AC3 16 LYS A 34 LYS A 56 ASN A 67 ARG A 68 SITE 3 AC3 16 GLU A 69 TYR A 75 MYR A1090 HOH A2014 SITE 4 AC3 16 HOH A2057 HOH A2074 HOH A2075 HOH A2076 SITE 1 AC4 6 LEU A 21 ASN A 23 LYS A 26 LEU A 29 SITE 2 AC4 6 TYR A 30 COA A1089 CRYST1 48.665 48.665 48.411 90.00 90.00 90.00 P 43 4 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 0.020549 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020656 0.00000