HEADER DE NOVO PROTEIN 28-OCT-14 4WSP TITLE RACEMIC CRYSTAL STRUCTURE OF RV1738 FROM MYCOBACTERIUM TUBERCULOSIS TITLE 2 (FORM-I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DL-RV1738; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 4 ORGANISM_TAXID: 83332 KEYWDS HYPOXIC RESPONSE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.D.BUNKER,K.MANDAL,S.B.H.KENT,E.N.BAKER REVDAT 5 27-SEP-23 4WSP 1 REMARK REVDAT 4 22-NOV-17 4WSP 1 SOURCE JRNL REMARK REVDAT 3 22-APR-15 4WSP 1 JRNL REVDAT 2 15-APR-15 4WSP 1 JRNL REVDAT 1 18-MAR-15 4WSP 0 JRNL AUTH R.D.BUNKER,K.MANDAL,G.BASHIRI,J.J.CHASTON,B.L.PENTELUTE, JRNL AUTH 2 J.S.LOTT,S.B.KENT,E.N.BAKER JRNL TITL A FUNCTIONAL ROLE OF RV1738 IN MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 PERSISTENCE SUGGESTED BY RACEMIC PROTEIN CRYSTALLOGRAPHY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 4310 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 25831534 JRNL DOI 10.1073/PNAS.1422387112 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1833 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 16914 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.330 REMARK 3 FREE R VALUE TEST SET COUNT : 1239 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 39.3548 - 3.4319 0.93 1657 134 0.2663 0.2524 REMARK 3 2 3.4319 - 2.7242 0.98 1758 130 0.2432 0.2602 REMARK 3 3 2.7242 - 2.3799 0.99 1766 133 0.2236 0.2338 REMARK 3 4 2.3799 - 2.1623 0.99 1741 160 0.2098 0.2610 REMARK 3 5 2.1623 - 2.0073 0.98 1748 141 0.2149 0.2671 REMARK 3 6 2.0073 - 1.8890 0.98 1753 134 0.2339 0.2739 REMARK 3 7 1.8890 - 1.7944 0.98 1747 126 0.2755 0.2665 REMARK 3 8 1.7944 - 1.7163 0.99 1760 145 0.3227 0.4032 REMARK 3 9 1.7163 - 1.6502 0.98 1745 136 0.3887 0.4603 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.47 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 : 0.009 650 REMARK 3 ANGLE : 1.067 884 REMARK 3 CHIRALITY : 0.056 106 REMARK 3 PLANARITY : 0.006 111 REMARK 3 DIHEDRAL : 14.454 248 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 4WSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000204408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-BM-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11, XDS JANUARY 10, REMARK 200 2014 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17584 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 47.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.84600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 4WPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICROLITRE OF PROTEIN SOLUTION REMARK 280 CONTAINING 9 MG/ML L-RV1738 AND 9 MG/ML D-RV1738 IN WATER WAS REMARK 280 MIXED WITH 1 MICROLITRE OF WELL SOLUTION CONTAINING 0.1 M BIS- REMARK 280 TRIS PH 5.5, 0.2 M NACL, 25 % (W/V) PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2/c 1 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 -X,-Y,-Z REMARK 290 4555 X,-Y,Z+1/2 REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 7555 -X+1/2,-Y+1/2,-Z REMARK 290 8555 X+1/2,-Y+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 -16.72005 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 23.82556 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 -16.72005 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.82556 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.06500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.20050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.34495 REMARK 290 SMTRY2 6 0.000000 1.000000 0.000000 16.20050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.82556 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.06500 REMARK 290 SMTRY2 7 0.000000 -1.000000 0.000000 16.20050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.34495 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 16.20050 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.82556 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 MET A 1 REMARK 465 CYS A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 50 REMARK 465 ASP A 51 REMARK 465 ARG A 52 REMARK 465 ASN A 53 REMARK 465 GLN A 88 REMARK 465 PRO A 89 REMARK 465 ALA A 90 REMARK 465 ARG A 91 REMARK 465 LEU A 92 REMARK 465 LEU A 93 REMARK 465 TYR A 94 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 GLN A 5 CG CD OE1 NE2 REMARK 470 VAL A 54 O 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 ARG A 35 -115.47 37.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WPY RELATED DB: PDB REMARK 900 4WPY IS A DIFFERENT CRYSTAL FORM OF THE SAME PROTEIN RACEMATE DBREF 4WSP A 1 94 UNP P9WLS3 Y1738_MYCTU 1 94 SEQRES 1 A 94 MET CYS GLY ASP GLN SER ASP HIS VAL LEU GLN HIS TRP SEQRES 2 A 94 THR VAL ASP ILE SER ILE ASP GLU HIS GLU GLY LEU THR SEQRES 3 A 94 ARG ALA LYS ALA ARG LEU ARG TRP ARG GLU LYS GLU LEU SEQRES 4 A 94 VAL GLY VAL GLY LEU ALA ARG LEU ASN PRO ALA ASP ARG SEQRES 5 A 94 ASN VAL PRO GLU ILE GLY ASP GLU LEU SER VAL ALA ARG SEQRES 6 A 94 ALA LEU SER ASP LEU GLY LYS ARG MET LEU LYS VAL SER SEQRES 7 A 94 THR HIS ASP ILE GLU ALA VAL THR HIS GLN PRO ALA ARG SEQRES 8 A 94 LEU LEU TYR HET CL A 101 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *18(H2 O) HELIX 1 AA1 PRO A 55 HIS A 87 1 33 SHEET 1 AA1 3 VAL A 15 HIS A 22 0 SHEET 2 AA1 3 LEU A 25 TRP A 34 -1 O ARG A 31 N ASP A 16 SHEET 3 AA1 3 LYS A 37 ARG A 46 -1 O LYS A 37 N TRP A 34 CRYST1 96.130 32.401 58.214 90.00 125.06 90.00 C 1 2/c 1 8 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 0.010403 0.000000 0.007300 0.00000 SCALE2 0.000000 0.030863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020986 0.00000