HEADER SIGNALING PROTEIN 07-MAR-16 5IMU TITLE A FRAGMENT OF CONSERVED HYPOTHETICAL PROTEIN RV3899C (RESIDUES 184- TITLE 2 410) FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAT (TWIN-ARGININE TRANSLOCATION) PATHWAY SIGNAL SEQUENCE COMPND 3 CONTAINING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 184-410; COMPND 6 SYNONYM: CONSERVED HYPOTHETICAL PROTEIN RV3899C, UNCHARACTERIZED COMPND 7 PROTEIN; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: RV3899C, LH57_21230; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS ALPHA/BETA/ALPHA SANDWICH, ALPHA HELIX BUNDULE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.F.LI,Y.R.GAO,Y.Y.LIU,L.J.BI REVDAT 2 20-MAR-24 5IMU 1 REMARK REVDAT 1 08-MAR-17 5IMU 0 JRNL AUTH Y.Y.LIU,Y.R.GAO,D.F.LI,J.FLEMING,H.L.LI,L.J.BI JRNL TITL CRYSTAL STRUCTURE OF RV3899C(184-410), A HYPOTHETICAL JRNL TITL 2 PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS JRNL REF ACTA CRYSTALLOGR F STRUCT V. 72 642 2016 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 27487929 JRNL DOI 10.1107/S2053230X16010943 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 16928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 850 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 44.5153 - 3.4521 1.00 2814 174 0.1404 0.1568 REMARK 3 2 3.4521 - 2.7402 1.00 2736 127 0.1545 0.1794 REMARK 3 3 2.7402 - 2.3938 1.00 2690 140 0.1692 0.2054 REMARK 3 4 2.3938 - 2.1750 1.00 2696 123 0.1597 0.2345 REMARK 3 5 2.1750 - 2.0191 1.00 2649 151 0.1760 0.2117 REMARK 3 6 2.0191 - 1.9000 0.95 2493 135 0.2241 0.2648 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.30 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 : 0.003 1677 REMARK 3 ANGLE : 0.616 2294 REMARK 3 CHIRALITY : 0.040 272 REMARK 3 PLANARITY : 0.004 301 REMARK 3 DIHEDRAL : 11.556 1019 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 5IMU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16973 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS REMARK 280 (PH 5.5), 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 25.07750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.90350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.48650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.90350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.07750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.48650 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 50 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 GLY A 184 REMARK 465 ALA A 185 REMARK 465 THR A 186 REMARK 465 GLY A 404 REMARK 465 SER A 405 REMARK 465 ARG A 406 REMARK 465 GLY A 407 REMARK 465 PHE A 408 REMARK 465 ALA A 409 REMARK 465 ALA A 410 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 O HOH A 842 O HOH A 924 1.97 REMARK 500 O HOH A 787 O HOH A 919 2.01 REMARK 500 O HOH A 915 O HOH A 944 2.01 REMARK 500 OH TYR A 387 O HOH A 601 2.04 REMARK 500 OD2 ASP A 259 O HOH A 602 2.18 REMARK 500 OD2 ASP A 264 O HOH A 603 2.19 REMARK 500 O HOH A 735 O HOH A 917 2.19 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 ALA A 234 64.12 -159.87 REMARK 500 SER A 363 33.83 -98.20 REMARK 500 GLN A 385 67.62 -106.92 REMARK 500 REMARK 500 REMARK: NULL 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 A 948 DISTANCE = 7.89 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 501 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 227 O REMARK 620 2 ASN A 247 O 84.3 REMARK 620 3 THR A 249 OG1 79.2 122.5 REMARK 620 4 HOH A 841 O 168.7 104.6 101.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 501 DBREF 5IMU A 184 410 UNP O05446 O05446_MYCTU 184 410 SEQRES 1 A 227 GLY ALA THR ALA GLY ALA VAL SER ALA ARG ALA ALA GLU SEQRES 2 A 227 GLN GLN ARG LEU GLN ARG ILE VAL ASP ALA VAL ALA ARG SEQRES 3 A 227 GLN GLU PRO ARG ILE SER TRP ALA ALA GLY LEU ARG ASP SEQRES 4 A 227 ASP GLY THR THR THR LEU LEU VAL THR ASP LEU ALA GLY SEQRES 5 A 227 GLY TRP ILE PRO PRO HIS VAL ARG LEU PRO ALA ASN VAL SEQRES 6 A 227 THR LEU LEU GLU PRO THR ALA ARG ARG ARG ASP ALA ASP SEQRES 7 A 227 VAL ILE ASP LEU LEU GLY ALA VAL VAL ALA VAL ALA ALA SEQRES 8 A 227 HIS GLU SER ASN THR TYR VAL ALA GLU PRO GLY PRO ASP SEQRES 9 A 227 ALA PRO ALA LEU THR GLY ASP ARG SER ALA ARG SER ALA SEQRES 10 A 227 ILE PRO LYS VAL ASP GLU PHE GLY PRO THR LEU VAL GLU SEQRES 11 A 227 ALA VAL ARG ARG ARG ASP SER LEU PRO ARG ILE ALA GLN SEQRES 12 A 227 ALA ILE ALA LEU PRO ALA VAL ARG LYS THR GLY VAL LEU SEQRES 13 A 227 GLU ASN GLU ALA GLU LEU LEU HIS GLY CYS ILE THR ALA SEQRES 14 A 227 VAL LYS GLU SER VAL LEU LYS ALA TYR PRO SER HIS GLU SEQRES 15 A 227 LEU THR ALA VAL GLY ASP TRP MET LEU LEU ALA ALA ILE SEQRES 16 A 227 GLU ALA LEU ILE ASP GLU GLN ASP TYR LEU ALA ASN TYR SEQRES 17 A 227 HIS LEU ALA TRP TYR ALA VAL THR THR ARG ARG GLY GLY SEQRES 18 A 227 SER ARG GLY PHE ALA ALA HET K A 501 1 HETNAM K POTASSIUM ION FORMUL 2 K K 1+ FORMUL 3 HOH *348(H2 O) HELIX 1 AA1 GLY A 188 GLU A 211 1 24 HELIX 2 AA2 ASP A 261 GLY A 267 1 7 HELIX 3 AA3 GLY A 293 SER A 299 1 7 HELIX 4 AA4 GLU A 306 ARG A 317 1 12 HELIX 5 AA5 PRO A 322 LYS A 335 1 14 HELIX 6 AA6 LEU A 339 TYR A 361 1 23 HELIX 7 AA7 GLU A 365 ASP A 383 1 19 HELIX 8 AA8 GLN A 385 THR A 400 1 16 SHEET 1 AA1 4 VAL A 248 LEU A 250 0 SHEET 2 AA1 4 THR A 227 THR A 231 1 N THR A 227 O THR A 249 SHEET 3 AA1 4 TRP A 216 LEU A 220 -1 N GLY A 219 O LEU A 228 SHEET 4 AA1 4 ALA A 271 HIS A 275 -1 O HIS A 275 N TRP A 216 LINK O THR A 227 K K A 501 1555 1555 3.48 LINK O ASN A 247 K K A 501 1555 1555 2.94 LINK OG1 THR A 249 K K A 501 1555 1555 2.79 LINK K K A 501 O HOH A 841 1555 1555 2.96 CISPEP 1 TYR A 361 PRO A 362 0 2.93 SITE 1 AC1 5 THR A 226 THR A 227 ASN A 247 THR A 249 SITE 2 AC1 5 HOH A 841 CRYST1 50.155 54.973 75.807 90.00 90.00 90.00 P 21 21 21 4 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 0.019938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013191 0.00000