HEADER LIPID BINDING PROTEIN 16-MAY-18 5ZWS TITLE CRYSTAL STRUCTURE OF APO-ACYL CARRIER PROTEIN FROM LEISHMANIA MAJOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL CARRIER PROTEIN; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: ACP, LMJF_27_0290; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LEISHMANIA MAJOR; ACYL CARRIER PROTEIN; FATTY ACID BIOSYNTHESIS, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ARYA,B.SHARMA,R.D.MAKDE,S.KUNDU REVDAT 2 22-NOV-23 5ZWS 1 REMARK REVDAT 1 16-JAN-19 5ZWS 0 JRNL AUTH R.ARYA,B.SHARMA,C.DHEMBLA,R.K.PAL,A.K.PATEL,M.SUNDD,B.GHOSH, JRNL AUTH 2 R.D.MAKDE,S.KUNDU JRNL TITL A CONFORMATIONAL SWITCH FROM A CLOSED APO- TO AN OPEN JRNL TITL 2 HOLO-FORM EQUIPS THE ACYL CARRIER PROTEIN FOR ACYL CHAIN JRNL TITL 3 ACCOMMODATION. JRNL REF BIOCHIM BIOPHYS ACTA V.1867 163 2018 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 30543875 JRNL DOI 10.1016/J.BBAPAP.2018.12.001 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.550 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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 11.5108 - 3.1590 0.94 2795 171 0.2376 0.2552 REMARK 3 2 3.1590 - 2.5160 0.96 2788 124 0.2635 0.3083 REMARK 3 3 2.5160 - 2.2005 0.93 2705 169 0.2571 0.2772 REMARK 3 4 2.2005 - 2.0005 0.92 2637 162 0.2583 0.2653 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1322 REMARK 3 ANGLE : 0.541 1795 REMARK 3 CHIRALITY : 0.043 214 REMARK 3 PLANARITY : 0.005 235 REMARK 3 DIHEDRAL : 15.320 813 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -25.9652 -5.1154 -14.3582 REMARK 3 T TENSOR REMARK 3 T11: 0.0055 T22: 0.0040 REMARK 3 T33: 0.0040 T12: 0.0042 REMARK 3 T13: 0.0003 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.0020 L22: 0.0013 REMARK 3 L33: 0.0034 L12: 0.0011 REMARK 3 L13: 0.0002 L23: 0.0002 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0005 S13: 0.0009 REMARK 3 S21: -0.0011 S22: -0.0005 S23: 0.0004 REMARK 3 S31: -0.0019 S32: -0.0014 S33: -0.0012 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 5ZWS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 FR-E+ DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11636 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52600 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 REMARK 200 STARTING MODEL: 1X3O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.5, 0.2M SODIUM REMARK 280 CHLORIDE, 25% W/V POLYETHELENE GLYCOL 3350, MICROBATCH, REMARK 280 TEMPERATURE 294K 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 23.72100 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 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 APPLY THE FOLLOWING TO CHAINS: B, 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 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 GLU A 16 CG CD OE1 OE2 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 PRO B 25 -9.71 -59.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2M5R RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HOLO-ACYL CARRIER PROTEIN DBREF 5ZWS B 3 80 UNP E9AD06 E9AD06_LEIMA 73 150 DBREF 5ZWS A 3 80 UNP E9AD06 E9AD06_LEIMA 73 150 SEQADV 5ZWS GLY B -2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS SER B -1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS HIS B 0 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS MET B 1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS ASN B 2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS GLY A -2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS SER A -1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS HIS A 0 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS MET A 1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWS ASN A 2 UNP E9AD06 EXPRESSION TAG SEQRES 1 B 83 GLY SER HIS MET ASN ASP VAL LEU THR ARG VAL LEU GLU SEQRES 2 B 83 VAL VAL LYS ASN PHE GLU LYS VAL ASP ALA SER LYS VAL SEQRES 3 B 83 THR PRO GLU SER HIS PHE VAL LYS ASP LEU GLY LEU ASN SEQRES 4 B 83 SER LEU ASP VAL VAL GLU VAL VAL PHE ALA ILE GLU GLN SEQRES 5 B 83 GLU PHE ILE LEU ASP ILE PRO ASP HIS ASP ALA GLU LYS SEQRES 6 B 83 ILE GLN SER ILE PRO ASP ALA VAL GLU TYR ILE ALA GLN SEQRES 7 B 83 ASN PRO MET ALA LYS SEQRES 1 A 83 GLY SER HIS MET ASN ASP VAL LEU THR ARG VAL LEU GLU SEQRES 2 A 83 VAL VAL LYS ASN PHE GLU LYS VAL ASP ALA SER LYS VAL SEQRES 3 A 83 THR PRO GLU SER HIS PHE VAL LYS ASP LEU GLY LEU ASN SEQRES 4 A 83 SER LEU ASP VAL VAL GLU VAL VAL PHE ALA ILE GLU GLN SEQRES 5 A 83 GLU PHE ILE LEU ASP ILE PRO ASP HIS ASP ALA GLU LYS SEQRES 6 A 83 ILE GLN SER ILE PRO ASP ALA VAL GLU TYR ILE ALA GLN SEQRES 7 A 83 ASN PRO MET ALA LYS FORMUL 3 HOH *10(H2 O) HELIX 1 AA1 SER B -1 PHE B 15 1 17 HELIX 2 AA2 ASP B 19 VAL B 23 5 5 HELIX 3 AA3 ASN B 36 PHE B 51 1 16 HELIX 4 AA4 PRO B 56 GLU B 61 1 6 HELIX 5 AA5 SER B 65 GLN B 75 1 11 HELIX 6 AA6 SER A -1 PHE A 15 1 17 HELIX 7 AA7 ASP A 19 VAL A 23 5 5 HELIX 8 AA8 ASN A 36 PHE A 51 1 16 HELIX 9 AA9 PRO A 56 GLU A 61 1 6 HELIX 10 AB1 SER A 65 ASN A 76 1 12 CRYST1 30.069 47.442 61.128 90.00 92.81 90.00 P 1 21 1 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 0.033257 0.000000 0.001635 0.00000 SCALE2 0.000000 0.021078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016379 0.00000