HEADER LIPID BINDING PROTEIN 14-JUL-21 7FC7 TITLE ACYL-COENZYME A BINDING PROTEIN 96 (LMJ_17_0780) OF LEISHMANIA MAJOR TITLE 2 IN COMPLEX WITH COENZYME A CAVEAT 7FC7 COA A 101 HAS WRONG CHIRALITY AT ATOM C1B COA A 101 HAS CAVEAT 2 7FC7 WRONG CHIRALITY AT ATOM C2B COA A 101 HAS WRONG CHIRALITY CAVEAT 3 7FC7 AT ATOM C4B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACB DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: LMJF_17_0780; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FATTY-ACYL-COA-BINDING PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VERMA,R.D.MAKDE,M.SUNDD REVDAT 2 29-NOV-23 7FC7 1 REMARK REVDAT 1 18-JAN-23 7FC7 0 JRNL AUTH S.VERMA,R.D.MAKDE,M.SUNDD JRNL TITL ACYL-COENZYME A BINDING PROTEIN 96 (LMJ_17_0780) OF JRNL TITL 2 LEISHMANIA MAJOR IN COMPLEX WITH COENZYME A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 4762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.325 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.010 REMARK 3 FREE R VALUE TEST SET COUNT : 191 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 2.2000 - 2.2000 0.99 4571 191 0.2689 0.3251 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) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.892 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.98 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 : 0.002 802 REMARK 3 ANGLE : 0.476 1099 REMARK 3 CHIRALITY : 0.037 117 REMARK 3 PLANARITY : 0.002 136 REMARK 3 DIHEDRAL : 18.216 299 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.0380 -3.1155 14.1698 REMARK 3 T TENSOR REMARK 3 T11: 0.7915 T22: 0.7961 REMARK 3 T33: 0.5812 T12: -0.2320 REMARK 3 T13: -0.0889 T23: 0.1182 REMARK 3 L TENSOR REMARK 3 L11: 3.2732 L22: 2.7880 REMARK 3 L33: 1.9338 L12: -2.9278 REMARK 3 L13: -0.1121 L23: 0.7202 REMARK 3 S TENSOR REMARK 3 S11: -0.3147 S12: -1.3837 S13: -0.0202 REMARK 3 S21: 0.7721 S22: 0.5549 S23: -0.2418 REMARK 3 S31: -0.2832 S32: -0.2972 S33: -0.3547 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8913 4.0120 5.8519 REMARK 3 T TENSOR REMARK 3 T11: 0.6034 T22: 0.3928 REMARK 3 T33: 0.3317 T12: -0.1347 REMARK 3 T13: -0.0389 T23: 0.0624 REMARK 3 L TENSOR REMARK 3 L11: 5.8500 L22: 6.6824 REMARK 3 L33: 4.8591 L12: -1.3413 REMARK 3 L13: -2.8740 L23: -2.2028 REMARK 3 S TENSOR REMARK 3 S11: 0.7446 S12: -0.0255 S13: 0.0281 REMARK 3 S21: 1.0104 S22: -0.4521 S23: 0.1168 REMARK 3 S31: -0.4704 S32: -0.6837 S33: -0.2110 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 42 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.6605 13.7281 6.9896 REMARK 3 T TENSOR REMARK 3 T11: 0.8004 T22: 0.5145 REMARK 3 T33: 0.4359 T12: -0.3051 REMARK 3 T13: -0.0867 T23: 0.0501 REMARK 3 L TENSOR REMARK 3 L11: 7.4886 L22: 4.0456 REMARK 3 L33: 6.3821 L12: -0.4159 REMARK 3 L13: -4.6179 L23: -3.4986 REMARK 3 S TENSOR REMARK 3 S11: 0.4540 S12: -0.9750 S13: -0.3419 REMARK 3 S21: 1.4281 S22: -0.3403 S23: -0.7622 REMARK 3 S31: 0.0150 S32: 0.7081 S33: 0.0212 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.6379 9.2754 21.5737 REMARK 3 T TENSOR REMARK 3 T11: 1.6290 T22: 1.1223 REMARK 3 T33: 0.5730 T12: -0.4154 REMARK 3 T13: -0.0577 T23: 0.0494 REMARK 3 L TENSOR REMARK 3 L11: 7.8659 L22: 6.0299 REMARK 3 L33: 2.0085 L12: -0.9758 REMARK 3 L13: -4.8027 L23: -6.1646 REMARK 3 S TENSOR REMARK 3 S11: 0.1910 S12: -1.7153 S13: 0.1915 REMARK 3 S21: 1.1709 S22: -0.1148 S23: -0.4322 REMARK 3 S31: -0.6673 S32: -0.8874 S33: 0.1773 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1353 3.7763 12.2240 REMARK 3 T TENSOR REMARK 3 T11: 0.6496 T22: 0.7454 REMARK 3 T33: 0.5101 T12: -0.1660 REMARK 3 T13: 0.0405 T23: 0.0463 REMARK 3 L TENSOR REMARK 3 L11: 8.5176 L22: 8.6708 REMARK 3 L33: 2.2220 L12: -4.5661 REMARK 3 L13: -1.8184 L23: -0.6861 REMARK 3 S TENSOR REMARK 3 S11: 0.1536 S12: 0.2102 S13: 0.2490 REMARK 3 S21: 0.4556 S22: -0.2499 S23: 1.5632 REMARK 3 S31: -0.9145 S32: -1.2384 S33: -0.1251 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 7FC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6348 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4000 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.91000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM ACETATE BUFFER PH 4.5, REMARK 280 200MM SODIUM CHLORIDE, 10MM MAGNESIUM CHLORIDE, 30% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K 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 25.78333 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 51.56667 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 51.56667 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 25.78333 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 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 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 41 CG CD OE1 OE2 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 GLN A 80 CG CD OE1 NE2 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 GLN A 53 81.51 -67.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FC7 A 1 96 UNP Q4QED0 Q4QED0_LEIMA 1 96 SEQRES 1 A 96 MET SER ALA ALA ASP PHE GLU ALA ALA VAL ALA TYR VAL SEQRES 2 A 96 ARG SER LEU PRO LYS ASP GLY PRO VAL GLN LEU ASP ASN SEQRES 3 A 96 ALA ALA LYS LEU GLN PHE TYR SER LEU TYR LYS GLN ALA SEQRES 4 A 96 THR GLU GLY ASP VAL THR GLY SER GLN PRO TRP ALA VAL SEQRES 5 A 96 GLN VAL GLU ALA ARG ALA LYS TRP ASP ALA TRP ASN SER SEQRES 6 A 96 CYS LYS GLY MET LYS SER GLU ASP ALA LYS ALA ALA TYR SEQRES 7 A 96 VAL GLN ARG LEU ILE GLU VAL THR SER GLN LYS GLY HIS SEQRES 8 A 96 PRO TRP ASN PRO ALA HET COA A 101 48 HETNAM COA COENZYME A FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 HOH *6(H2 O) HELIX 1 AA1 SER A 2 SER A 15 1 14 HELIX 2 AA2 ASP A 25 GLU A 41 1 17 HELIX 3 AA3 GLN A 53 CYS A 66 1 14 HELIX 4 AA4 LYS A 70 GLN A 88 1 19 CRYST1 44.376 44.376 77.350 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 0.022535 0.013010 0.000000 0.00000 SCALE2 0.000000 0.026021 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012928 0.00000