HEADER LIPID BINDING PROTEIN 27-DEC-21 7WFS TITLE ACYL-COENZYME A BINDING PROTEIN 103 (LMJF_17_0620) OF LEISHMANIA MAJOR TITLE 2 IN TRICLINIC CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACB DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: LMJF_17_0620; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS ACYL-COENZYME A BINDING PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VERMA,M.SUNDD REVDAT 2 29-NOV-23 7WFS 1 REMARK REVDAT 1 01-FEB-23 7WFS 0 JRNL AUTH S.VERMA,M.SUNDD JRNL TITL ACYL-COENZYME A BINDING PROTEIN 103 (LMJF_17_0620) OF JRNL TITL 2 LEISHMANIA MAJOR IN MONOCLINIC CRYSTAL FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 35717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 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 22.7300 - 3.2900 0.93 2589 153 0.1903 0.2421 REMARK 3 2 3.2900 - 2.6100 0.96 2683 144 0.2113 0.2278 REMARK 3 3 2.6100 - 2.2800 0.96 2713 124 0.2093 0.1823 REMARK 3 4 2.2800 - 2.0700 0.96 2703 106 0.2011 0.2756 REMARK 3 5 2.0700 - 1.9300 0.96 2732 110 0.2248 0.3081 REMARK 3 6 1.9200 - 1.8100 0.95 2619 154 0.2545 0.2775 REMARK 3 7 1.8100 - 1.7200 0.94 2653 159 0.2551 0.2793 REMARK 3 8 1.7200 - 1.6500 0.93 2573 170 0.2767 0.2854 REMARK 3 9 1.6500 - 1.5800 0.92 2545 144 0.2734 0.2822 REMARK 3 10 1.5800 - 1.5300 0.92 2556 170 0.3295 0.3679 REMARK 3 11 1.5300 - 1.4800 0.89 2502 140 0.3793 0.3502 REMARK 3 12 1.4800 - 1.4400 0.90 2504 153 0.4066 0.4310 REMARK 3 13 1.4400 - 1.4000 0.88 2464 154 0.4601 0.5058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.306 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.076 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.65 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 : 0.009 1547 REMARK 3 ANGLE : 0.983 2106 REMARK 3 CHIRALITY : 0.066 224 REMARK 3 PLANARITY : 0.007 272 REMARK 3 DIHEDRAL : 17.884 554 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7WFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026606. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979490 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36124 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 7DES REMARK 200 REMARK 200 REMARK: ROD-SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRISCL 2M AMMONIUM SULFATE, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 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 GLY A 97 REMARK 465 ALA A 98 REMARK 465 ARG A 99 REMARK 465 VAL A 100 REMARK 465 GLN A 101 REMARK 465 SER A 102 REMARK 465 ARG A 103 REMARK 465 GLY B 97 REMARK 465 ALA B 98 REMARK 465 ARG B 99 REMARK 465 VAL B 100 REMARK 465 GLN B 101 REMARK 465 SER B 102 REMARK 465 ARG B 103 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 LYS A 18 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS B 18 CG CD CE NZ REMARK 470 GLN B 92 CG CD OE1 NE2 REMARK 470 LYS B 94 CG CD CE 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 B 286 DISTANCE = 5.96 ANGSTROMS DBREF 7WFS A 1 103 UNP Q4QED2 Q4QED2_LEIMA 1 102 DBREF 7WFS B 1 103 UNP Q4QED2 Q4QED2_LEIMA 1 102 SEQADV 7WFS HIS A 0 UNP Q4QED2 EXPRESSION TAG SEQADV 7WFS GLY A 96 UNP Q4QED2 INSERTION SEQADV 7WFS HIS B 0 UNP Q4QED2 EXPRESSION TAG SEQADV 7WFS GLY B 96 UNP Q4QED2 INSERTION SEQRES 1 A 104 HIS MET SER ALA ALA ASP PHE GLU ALA ALA VAL ALA TYR SEQRES 2 A 104 VAL ARG SER LEU PRO LYS ASP GLY PRO VAL GLN LEU ASP SEQRES 3 A 104 ASN ALA ALA LYS LEU GLN PHE TYR SER LEU TYR LYS GLN SEQRES 4 A 104 ALA THR GLU GLY ASP VAL THR GLY SER GLN PRO TRP ALA SEQRES 5 A 104 VAL GLN VAL GLU ALA ARG ALA LYS TRP ASP ALA TRP ASN SEQRES 6 A 104 SER CYS LYS GLY MET LYS SER GLU ASP ALA LYS ALA ALA SEQRES 7 A 104 TYR VAL ARG ARG LEU LEU THR LEU LEU ARG SER GLN GLY SEQRES 8 A 104 ILE GLN TRP LYS PRO GLY GLY ALA ARG VAL GLN SER ARG SEQRES 1 B 104 HIS MET SER ALA ALA ASP PHE GLU ALA ALA VAL ALA TYR SEQRES 2 B 104 VAL ARG SER LEU PRO LYS ASP GLY PRO VAL GLN LEU ASP SEQRES 3 B 104 ASN ALA ALA LYS LEU GLN PHE TYR SER LEU TYR LYS GLN SEQRES 4 B 104 ALA THR GLU GLY ASP VAL THR GLY SER GLN PRO TRP ALA SEQRES 5 B 104 VAL GLN VAL GLU ALA ARG ALA LYS TRP ASP ALA TRP ASN SEQRES 6 B 104 SER CYS LYS GLY MET LYS SER GLU ASP ALA LYS ALA ALA SEQRES 7 B 104 TYR VAL ARG ARG LEU LEU THR LEU LEU ARG SER GLN GLY SEQRES 8 B 104 ILE GLN TRP LYS PRO GLY GLY ALA ARG VAL GLN SER ARG FORMUL 3 HOH *163(H2 O) HELIX 1 AA1 SER A 2 ALA A 4 5 3 HELIX 2 AA2 ASP A 5 LEU A 16 1 12 HELIX 3 AA3 ASP A 25 GLY A 42 1 18 HELIX 4 AA4 GLN A 53 SER A 65 1 13 HELIX 5 AA5 LYS A 70 SER A 88 1 19 HELIX 6 AA6 SER B 2 ALA B 4 5 3 HELIX 7 AA7 ASP B 5 LEU B 16 1 12 HELIX 8 AA8 ASP B 25 GLY B 42 1 18 HELIX 9 AA9 GLN B 53 SER B 65 1 13 HELIX 10 AB1 LYS B 70 GLN B 89 1 20 CRYST1 37.258 37.980 45.975 89.68 66.13 60.72 P 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 0.026840 -0.015051 -0.015980 0.00000 SCALE2 0.000000 0.030187 0.007501 0.00000 SCALE3 0.000000 0.000000 0.024509 0.00000