HEADER HYDROLASE 09-SEP-21 7VEP TITLE CRYSTAL STRUCTURE AND BIOPHYSICAL CHARACTERIZATION OF TPR DOMAIN OF TITLE 2 ECCA5 FROM ESX-5 PATHWAY OF MYCOBACTERIUM TUBERCULOSIS H37RVR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESX-5 SECRETION SYSTEM PROTEIN ECCA5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ESX CONSERVED COMPONENT A5,TYPE VII SECRETION SYSTEM PROTEIN COMPND 5 ECCA5,T7SS PROTEIN ECCA5; COMPND 6 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: ECCA5, RV1798, MTV049.20; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A KEYWDS ECCA5, AAA+ATPASE, TPR DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.RAMACHANDRAN,V.K.SHARMA,J.VISHWAKARMA REVDAT 1 14-SEP-22 7VEP 0 JRNL AUTH R.RAMACHANDRAN,V.K.SHARMA,J.VISHWAKARMA JRNL TITL CRYSTAL STRUCTURE AND BIOPHYSICAL CHARACTERIZATION OF TPR JRNL TITL 2 DOMAIN OF ECCA5 FROM ESX-5 PATHWAY OF MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS H37RVR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 993 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 39.3000 - 4.1115 1.00 2941 164 0.1767 0.1818 REMARK 3 2 4.1115 - 3.2639 0.99 2822 155 0.1587 0.1895 REMARK 3 3 3.2639 - 2.8515 0.99 2790 147 0.1935 0.2511 REMARK 3 4 2.8515 - 2.5908 0.99 2776 133 0.1986 0.2436 REMARK 3 5 2.5908 - 2.4051 0.99 2764 128 0.2000 0.2362 REMARK 3 6 2.4051 - 2.2633 0.99 2748 140 0.2195 0.2879 REMARK 3 7 2.2633 - 2.1500 0.98 2702 126 0.2332 0.2729 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.04 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7VEP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.70 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0.072 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20585 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 43.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.63100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 2.8.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: 3D ROD SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, SODIUM CITRATE 5.6, REMARK 280 AMMONIUM SULFATE, GLYCEROL AS ADDITIVE, PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 300K 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 28.61800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.10200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.82250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.10200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.61800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.82250 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 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 1 REMARK 465 SER A 2 REMARK 465 THR A 277 REMARK 465 ILE A 278 REMARK 465 GLU A 279 REMARK 465 ALA A 280 REMARK 465 ARG A 281 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 HIS A 3 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 33 CG CD OE1 NE2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 ARG A 269 CG CD NE CZ NH1 NH2 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 533 O HOH A 545 1.77 REMARK 500 O HOH A 526 O HOH A 539 1.85 REMARK 500 O HOH A 426 O HOH A 544 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 498 O HOH A 521 3454 2.18 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 LEU A 105 -55.98 -132.45 REMARK 500 PHE A 106 -40.73 -134.25 REMARK 500 THR A 141 -64.85 -101.83 REMARK 500 ARG A 269 55.59 -150.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VEP A 4 281 UNP P9WPI1 ECCA5_MYCTU 1 278 SEQADV 7VEP GLY A 1 UNP P9WPI1 EXPRESSION TAG SEQADV 7VEP SER A 2 UNP P9WPI1 EXPRESSION TAG SEQADV 7VEP HIS A 3 UNP P9WPI1 EXPRESSION TAG SEQRES 1 A 281 GLY SER HIS MET THR ARG PRO GLN ALA ALA ALA GLU ASP SEQRES 2 A 281 ALA ARG ASN ALA MET VAL ALA GLY LEU LEU ALA SER GLY SEQRES 3 A 281 ILE SER VAL ASN GLY LEU GLN PRO SER HIS ASN PRO GLN SEQRES 4 A 281 VAL ALA ALA GLN MET PHE THR THR ALA THR ARG LEU ASP SEQRES 5 A 281 PRO LYS MET CYS ASP ALA TRP LEU ALA ARG LEU LEU ALA SEQRES 6 A 281 GLY ASP GLN SER ILE GLU VAL LEU ALA GLY ALA TRP ALA SEQRES 7 A 281 ALA VAL ARG THR PHE GLY TRP GLU THR ARG ARG LEU GLY SEQRES 8 A 281 VAL THR ASP LEU GLN PHE ARG PRO GLU VAL SER ASP GLY SEQRES 9 A 281 LEU PHE LEU ARG LEU ALA ILE THR SER VAL ASP SER LEU SEQRES 10 A 281 ALA CYS ALA TYR ALA ALA VAL LEU ALA GLU ALA LYS ARG SEQRES 11 A 281 TYR GLN GLU ALA ALA GLU LEU LEU ASP ALA THR ASP PRO SEQRES 12 A 281 ARG HIS PRO PHE ASP ALA GLU LEU VAL SER TYR VAL ARG SEQRES 13 A 281 GLY VAL LEU TYR PHE ARG THR LYS ARG TRP PRO ASP VAL SEQRES 14 A 281 LEU ALA GLN PHE PRO GLU ALA THR GLN TRP ARG HIS PRO SEQRES 15 A 281 GLU LEU LYS ALA ALA GLY ALA ALA MET ALA THR THR ALA SEQRES 16 A 281 LEU ALA SER LEU GLY VAL PHE GLU GLU ALA PHE ARG ARG SEQRES 17 A 281 ALA GLN GLU ALA ILE GLU GLY ASP ARG VAL PRO GLY ALA SEQRES 18 A 281 ALA ASN ILE ALA LEU TYR THR GLN GLY MET CYS LEU ARG SEQRES 19 A 281 HIS VAL GLY ARG GLU GLU GLU ALA VAL GLU LEU LEU ARG SEQRES 20 A 281 ARG VAL TYR SER ARG ASP ALA LYS PHE THR PRO ALA ARG SEQRES 21 A 281 GLU ALA LEU ASP ASN PRO ASN PHE ARG LEU ILE LEU THR SEQRES 22 A 281 ASP PRO GLU THR ILE GLU ALA ARG HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET GOL A 304 14 HET GOL A 305 14 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *150(H2 O) HELIX 1 AA1 THR A 5 ALA A 24 1 20 HELIX 2 AA2 ASN A 37 ASP A 52 1 16 HELIX 3 AA3 MET A 55 ALA A 65 1 11 HELIX 4 AA4 SER A 69 ALA A 79 1 11 HELIX 5 AA5 VAL A 80 PHE A 83 5 4 HELIX 6 AA6 GLY A 84 GLY A 91 1 8 HELIX 7 AA7 SER A 113 ALA A 128 1 16 HELIX 8 AA8 ARG A 130 ALA A 140 1 11 HELIX 9 AA9 HIS A 145 THR A 163 1 19 HELIX 10 AB1 ARG A 165 PHE A 173 1 9 HELIX 11 AB2 HIS A 181 LEU A 199 1 19 HELIX 12 AB3 VAL A 201 GLU A 214 1 14 HELIX 13 AB4 GLY A 215 ARG A 217 5 3 HELIX 14 AB5 VAL A 218 VAL A 236 1 19 HELIX 15 AB6 ARG A 238 ASP A 253 1 16 HELIX 16 AB7 PHE A 256 ASN A 265 1 10 SHEET 1 AA1 2 GLU A 100 SER A 102 0 SHEET 2 AA1 2 ARG A 108 ALA A 110 -1 O LEU A 109 N VAL A 101 CRYST1 57.236 65.645 98.204 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 0.017472 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010183 0.00000