HEADER DE NOVO PROTEIN 21-OCT-14 4WPY TITLE RACEMIC CRYSTAL STRUCTURE OF RV1738 FROM MYCOBACTERIUM TUBERCULOSIS TITLE 2 (FORM-II) 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 H37RV; 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 6 27-DEC-23 4WPY 1 REMARK REVDAT 5 22-NOV-17 4WPY 1 REMARK REVDAT 4 06-SEP-17 4WPY 1 SOURCE JRNL REMARK REVDAT 3 22-APR-15 4WPY 1 JRNL REVDAT 2 15-APR-15 4WPY 1 JRNL REVDAT 1 18-MAR-15 4WPY 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.870 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 28131 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2205 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 37.3614 - 3.7786 0.99 1614 132 0.2278 0.2226 REMARK 3 2 3.7786 - 2.9996 1.00 1625 136 0.1926 0.2068 REMARK 3 3 2.9996 - 2.6205 1.00 1634 124 0.2004 0.2132 REMARK 3 4 2.6205 - 2.3810 1.00 1646 119 0.1883 0.2249 REMARK 3 5 2.3810 - 2.2103 1.00 1592 152 0.1966 0.2167 REMARK 3 6 2.2103 - 2.0800 1.00 1617 143 0.1799 0.2440 REMARK 3 7 2.0800 - 1.9759 0.99 1597 152 0.1924 0.2627 REMARK 3 8 1.9759 - 1.8899 1.00 1638 132 0.1877 0.2241 REMARK 3 9 1.8899 - 1.8171 1.00 1624 138 0.2354 0.2445 REMARK 3 10 1.8171 - 1.7544 1.00 1616 119 0.2515 0.3219 REMARK 3 11 1.7544 - 1.6995 1.00 1620 147 0.2932 0.3598 REMARK 3 12 1.6995 - 1.6510 1.00 1630 149 0.3242 0.3685 REMARK 3 13 1.6510 - 1.6075 1.00 1616 147 0.3513 0.3703 REMARK 3 14 1.6075 - 1.5683 1.00 1604 137 0.3675 0.4329 REMARK 3 15 1.5683 - 1.5326 1.00 1595 152 0.4216 0.4242 REMARK 3 16 1.5326 - 1.5000 1.00 1658 126 0.4784 0.5336 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.97 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 : 0.011 751 REMARK 3 ANGLE : 1.020 1023 REMARK 3 CHIRALITY : 0.051 117 REMARK 3 PLANARITY : 0.006 132 REMARK 3 DIHEDRAL : 13.616 294 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 4WPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000204284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-09 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 : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29319 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 51.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.65200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: IDEALIZED 14MER POLYALA HELIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 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, 25 % (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 -13.91497 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 25.69230 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 -13.91497 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.69230 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.20100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.99450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.28603 REMARK 290 SMTRY2 6 0.000000 1.000000 0.000000 21.99450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.69230 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.20100 REMARK 290 SMTRY2 7 0.000000 -1.000000 0.000000 21.99450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.28603 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 21.99450 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.69230 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 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -13.91497 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 25.69230 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 GLN A 5 REMARK 465 SER A 6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HE ARG A 31 HO2 GOL A 102 1.20 REMARK 500 O HOH A 252 O HOH A 270 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 -110.74 30.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WSP RELATED DB: PDB DBREF 4WPY A 1 94 UNP P9WLS2 Y1738_MYCTO 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 TFA A 101 7 HET GOL A 102 14 HETNAM TFA TRIFLUOROACETIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 TFA C2 H F3 O2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *84(H2 O) HELIX 1 AA1 ASN A 48 ARG A 52 5 5 HELIX 2 AA2 VAL A 54 HIS A 87 1 34 SHEET 1 AA1 3 ASP A 16 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 80.402 43.989 58.437 90.00 118.44 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 0.012438 0.000000 0.006735 0.00000 SCALE2 0.000000 0.022733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019460 0.00000