HEADER LIPID TRANSPORT 24-OCT-19 6T84 TITLE CRYSTAL STRUCTURE OF THE MYCOBACTERIAL TREHALOSE MONOMYCOLATE TITLE 2 TRANSPORT FACTOR A, TTFA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GHM IN N-TERMINUS IS A TAG AS WELL AS AS IN C-TERMINUS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 GENE: MSMEG_0736; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS TREHALOSE MONOMYCOLATE, MMPL3 ACCESSORY PROTEIN, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.BLAISE REVDAT 3 15-MAY-24 6T84 1 REMARK REVDAT 2 27-MAY-20 6T84 1 JRNL REVDAT 1 25-DEC-19 6T84 0 JRNL AUTH K.L.UNG,H.M.A.B.ALSARRAF,L.KREMER,M.BLAISE JRNL TITL THE CRYSTAL STRUCTURE OF THE MYCOBACTERIAL TREHALOSE JRNL TITL 2 MONOMYCOLATE TRANSPORT FACTOR A, TTFA, REVEALS AN ATYPICAL JRNL TITL 3 FOLD. JRNL REF PROTEINS V. 88 809 2020 JRNL REFN ESSN 1097-0134 JRNL PMID 31833106 JRNL DOI 10.1002/PROT.25863 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37306 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1865 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 46.5400 - 3.2900 1.00 2886 152 0.1610 0.1677 REMARK 3 2 3.2900 - 2.6100 1.00 2766 146 0.1770 0.2054 REMARK 3 3 2.6100 - 2.2800 1.00 2752 145 0.1815 0.1994 REMARK 3 4 2.2800 - 2.0700 1.00 2738 144 0.1574 0.2011 REMARK 3 5 2.0700 - 1.9200 1.00 2715 143 0.1556 0.1903 REMARK 3 6 1.9200 - 1.8100 1.00 2704 142 0.1635 0.2059 REMARK 3 7 1.8100 - 1.7200 1.00 2704 143 0.1659 0.2073 REMARK 3 8 1.7200 - 1.6500 1.00 2730 143 0.1774 0.2035 REMARK 3 9 1.6500 - 1.5800 1.00 2695 141 0.1869 0.2212 REMARK 3 10 1.5800 - 1.5300 1.00 2681 141 0.2012 0.2381 REMARK 3 11 1.5300 - 1.4800 1.00 2691 142 0.2366 0.2655 REMARK 3 12 1.4800 - 1.4400 1.00 2694 142 0.2643 0.3142 REMARK 3 13 1.4400 - 1.4000 0.99 2685 141 0.2946 0.3124 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) : 0.164 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.849 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.14 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 : 0.013 1592 REMARK 3 ANGLE : 1.233 2176 REMARK 3 CHIRALITY : 0.110 234 REMARK 3 PLANARITY : 0.007 287 REMARK 3 DIHEDRAL : 12.988 614 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 6T84 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292105041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05072 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.11800 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 4000 AND 0.2 M (NH4)2SO4, PH REMARK 280 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 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 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 -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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 31.12000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.04500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.00500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.12000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.04500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.00500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.12000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.04500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.00500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.12000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.04500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.00500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 A 509 LIES ON A SPECIAL POSITION. 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 21 REMARK 465 HIS A 22 REMARK 465 MET A 23 REMARK 465 ILE A 24 REMARK 465 ASP A 25 REMARK 465 ARG A 26 REMARK 465 ASN A 205 REMARK 465 ALA A 206 REMARK 465 SER A 207 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 58 -162.83 -116.66 REMARK 500 VAL A 90 -60.61 -126.70 REMARK 500 GLU A 165 -166.02 -121.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 DBREF 6T84 A 24 205 UNP A0QQF4 A0QQF4_MYCS2 24 205 SEQADV 6T84 GLY A 21 UNP A0QQF4 EXPRESSION TAG SEQADV 6T84 HIS A 22 UNP A0QQF4 EXPRESSION TAG SEQADV 6T84 MET A 23 UNP A0QQF4 EXPRESSION TAG SEQADV 6T84 ALA A 206 UNP A0QQF4 EXPRESSION TAG SEQADV 6T84 SER A 207 UNP A0QQF4 EXPRESSION TAG SEQRES 1 A 187 GLY HIS MET ILE ASP ARG ARG ARG GLY LEU GLY ARG ARG SEQRES 2 A 187 ARG LYS SER TRP ALA LYS SER HIS GLY PHE ASP TYR GLU SEQRES 3 A 187 TYR GLU SER GLU ASP LEU LEU LYS ARG TRP LYS ARG GLY SEQRES 4 A 187 VAL MET SER THR VAL GLY ASP VAL THR ALA LYS ASN VAL SEQRES 5 A 187 VAL LEU GLY GLN ILE ARG GLY GLU ALA VAL PHE ILE PHE SEQRES 6 A 187 ASP ILE GLU GLU VAL ALA THR VAL ILE ALA LEU HIS ARG SEQRES 7 A 187 LYS VAL GLY THR ASN VAL VAL VAL ASP LEU ARG LEU LYS SEQRES 8 A 187 GLY LEU LYS GLU PRO ARG GLU ASN ASP ILE TRP LEU LEU SEQRES 9 A 187 GLY ALA ILE GLY PRO ARG MET VAL TYR SER THR ASN LEU SEQRES 10 A 187 ASP ALA ALA ARG ARG ALA CYS ASP ARG ARG MET VAL THR SEQRES 11 A 187 PHE ALA HIS THR ALA PRO ASP CYS ALA GLU ILE MET TRP SEQRES 12 A 187 ASN GLU GLN ASN TRP THR LEU VAL ALA MET PRO VAL THR SEQRES 13 A 187 SER ASN ARG ALA GLN TRP ASP GLU GLY LEU ARG THR VAL SEQRES 14 A 187 ARG GLN PHE ASN ASP LEU LEU ARG VAL LEU PRO PRO VAL SEQRES 15 A 187 PRO GLN ASN ALA SER HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *183(H2 O) HELIX 1 AA1 GLY A 29 GLY A 42 1 14 HELIX 2 AA2 ASP A 51 TRP A 56 5 6 HELIX 3 AA3 ARG A 58 SER A 62 5 5 HELIX 4 AA4 ASN A 136 CYS A 144 1 9 HELIX 5 AA5 ASP A 145 ALA A 155 1 11 HELIX 6 AA6 ASN A 178 LEU A 196 1 19 HELIX 7 AA7 ARG A 197 LEU A 199 5 3 SHEET 1 AA1 9 ASP A 44 SER A 49 0 SHEET 2 AA1 9 ALA A 69 ILE A 77 -1 O VAL A 72 N GLU A 46 SHEET 3 AA1 9 GLU A 80 ILE A 87 -1 O ILE A 84 N VAL A 73 SHEET 4 AA1 9 ALA A 91 HIS A 97 -1 O HIS A 97 N ALA A 81 SHEET 5 AA1 9 TRP A 168 MET A 173 -1 O THR A 169 N LEU A 96 SHEET 6 AA1 9 ILE A 161 ASN A 164 -1 N TRP A 163 O LEU A 170 SHEET 7 AA1 9 VAL A 106 LEU A 110 -1 N LEU A 108 O MET A 162 SHEET 8 AA1 9 ARG A 130 SER A 134 -1 O TYR A 133 N ASP A 107 SHEET 9 AA1 9 TRP A 122 ILE A 127 -1 N ILE A 127 O ARG A 130 SITE 1 AC1 8 GLY A 29 LEU A 30 GLY A 31 ARG A 32 SITE 2 AC1 8 ASP A 145 ARG A 146 HOH A 404 HOH A 408 SITE 1 AC2 6 ARG A 55 ASN A 119 ASN A 167 TRP A 168 SITE 2 AC2 6 HOH A 403 HOH A 440 CRYST1 62.240 70.090 86.010 90.00 90.00 90.00 I 2 2 2 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 0.016067 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011627 0.00000