HEADER LIPID BINDING PROTEIN 16-MAY-18 5ZWT TITLE CRYSTAL STRUCTURE OF THE S37A MUTANT OF APO-ACYL CARRIER PROTEIN FROM TITLE 2 LEISHMANIA MAJOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL CARRIER PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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 B.SHARMA,R.ARYA,S.KUNDU,R.D.MAKDE REVDAT 2 22-NOV-23 5ZWT 1 REMARK REVDAT 1 16-JAN-19 5ZWT 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) : 31.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 11637 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 578 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 31.9974 - 3.1740 0.95 2904 149 0.2027 0.2498 REMARK 3 2 3.1740 - 2.5196 1.00 2880 157 0.2609 0.3001 REMARK 3 3 2.5196 - 2.2012 0.84 2420 120 0.2965 0.3254 REMARK 3 4 2.2012 - 2.0000 1.00 2855 152 0.2830 0.2656 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.400 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 : 0.007 1267 REMARK 3 ANGLE : 0.877 1728 REMARK 3 CHIRALITY : 0.059 214 REMARK 3 PLANARITY : 0.009 227 REMARK 3 DIHEDRAL : 18.227 770 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): -24.7773 -2.0873 -25.8077 REMARK 3 T TENSOR REMARK 3 T11: 0.2616 T22: 0.2709 REMARK 3 T33: 0.2368 T12: 0.0551 REMARK 3 T13: 0.0273 T23: 0.0323 REMARK 3 L TENSOR REMARK 3 L11: 0.6322 L22: 1.7695 REMARK 3 L33: 1.5539 L12: -0.1367 REMARK 3 L13: 0.5033 L23: -1.3833 REMARK 3 S TENSOR REMARK 3 S11: 0.1236 S12: -0.1018 S13: -0.0218 REMARK 3 S21: -0.2599 S22: -0.0249 S23: 0.1912 REMARK 3 S31: 0.1032 S32: 0.6184 S33: 0.2689 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 5ZWT 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_1300007793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11845 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 41.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 0.95600 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 (%): 47.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 2.0M AMMONIUM REMARK 280 SULPHATE, MICROBATCH, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 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 0.00000 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 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 41.75300 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 49.79200 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 41.75300 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 49.79200 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 41.75300 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 49.79200 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 41.75300 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 49.79200 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 41.75300 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 49.79200 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 41.75300 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 49.79200 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 41.75300 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 49.79200 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 41.75300 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 41.75300 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 49.79200 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 113 LIES ON A SPECIAL POSITION. 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 CD OE1 OE2 REMARK 470 LYS A 17 CD CE NZ REMARK 470 HIS A 58 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 PRO A 77 CG CD REMARK 470 MET A 78 CG SD CE REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 ASN B 14 CG OD1 ND2 REMARK 470 HIS B 58 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 GLN B 75 CG CD OE1 NE2 REMARK 470 PRO B 77 CG CD REMARK 470 MET B 78 CG SD CE REMARK 470 LYS B 80 CG CD CE NZ REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2M5R RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HOLO-ACYL CARRIER PROTEIN DBREF 5ZWT A 3 80 UNP E9AD06 E9AD06_LEIMA 73 150 DBREF 5ZWT B 3 80 UNP E9AD06 E9AD06_LEIMA 73 150 SEQADV 5ZWT GLY A -2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT SER A -1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT HIS A 0 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT MET A 1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT ASN A 2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT ALA A 37 UNP E9AD06 SER 107 ENGINEERED MUTATION SEQADV 5ZWT GLY B -2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT SER B -1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT HIS B 0 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT MET B 1 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT ASN B 2 UNP E9AD06 EXPRESSION TAG SEQADV 5ZWT ALA B 37 UNP E9AD06 SER 107 ENGINEERED MUTATION 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 ALA 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 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 ALA 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 FORMUL 3 HOH *72(H2 O) HELIX 1 AA1 SER A -1 ASN A 14 1 16 HELIX 2 AA2 ASP A 19 VAL A 23 5 5 HELIX 3 AA3 ASN A 36 PHE A 51 1 16 HELIX 4 AA4 PRO A 56 GLU A 61 1 6 HELIX 5 AA5 SER A 65 ASN A 76 1 12 HELIX 6 AA6 SER B -1 PHE B 15 1 17 HELIX 7 AA7 ASP B 19 VAL B 23 5 5 HELIX 8 AA8 ASN B 36 PHE B 51 1 16 HELIX 9 AA9 PRO B 56 GLU B 61 1 6 HELIX 10 AB1 SER B 65 ASN B 76 1 12 CRYST1 83.506 83.506 99.584 90.00 90.00 90.00 I 4 2 2 32 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 0.011975 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011975 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010042 0.00000