HEADER TRANSPORT PROTEIN 19-JUN-20 6ZGN TITLE CRYSTAL STRUCTURE OF VIRB8-LIKE ORFG CENTRAL DOMAIN OF STREPTOCOCCUS TITLE 2 THERMOPHILUS ICEST3; A PUTATIVE ASSEMBLY FACTOR OF A GRAM POSITIVE TITLE 3 CONJUGATIVE TYPE IV SECRETION SYSTEM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TRANSFER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1308; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS NTF2-LIKE, VIRB8-LIKE, TRANSPORT PROTEIN, TYPE IV SECRETION SYSTEM, KEYWDS 2 GRAM POSITIVE EXPDTA X-RAY DIFFRACTION AUTHOR J.CAPPELE,A.MOHAMAD-ALI,N.LEBLOND-BOURGET,S.PAYOT-LACROIX,S.MATHIOT, AUTHOR 2 C.DIDIERJEAN,F.FAVIER,B.DOUZI REVDAT 2 15-MAY-24 6ZGN 1 REMARK REVDAT 1 28-APR-21 6ZGN 0 JRNL AUTH J.CAPPELE,A.MOHAMAD ALI,N.LEBLOND-BOURGET,S.MATHIOT, JRNL AUTH 2 T.DHALLEINE,S.PAYOT,M.SAVKO,C.DIDIERJEAN,F.FAVIER,B.DOUZI JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSIS OF ORFG: THE VIRB8-LIKE JRNL TITL 2 COMPONENT OF THE CONJUGATIVE TYPE IV SECRETION SYSTEM OF ICE JRNL TITL 3 ST3 FROM STREPTOCOCCUS THERMOPHILUS . JRNL REF FRONT MOL BIOSCI V. 8 42606 2021 JRNL REFN ESSN 2296-889X JRNL PMID 33816557 JRNL DOI 10.3389/FMOLB.2021.642606 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16309 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 835 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 46.3310 - 7.7220 0.98 224 12 0.2800 0.2880 REMARK 3 2 7.7220 - 5.4990 1.00 351 26 0.2850 0.2540 REMARK 3 3 5.4990 - 4.5000 1.00 437 26 0.1850 0.1670 REMARK 3 4 4.5000 - 3.9020 1.00 517 24 0.1610 0.1840 REMARK 3 5 3.9020 - 3.4930 1.00 568 40 0.1830 0.1750 REMARK 3 6 3.4930 - 3.1900 1.00 637 19 0.1950 0.1780 REMARK 3 7 3.1900 - 2.9540 1.00 651 43 0.1970 0.2500 REMARK 3 8 2.9540 - 2.7640 1.00 738 34 0.2110 0.1540 REMARK 3 9 2.7640 - 2.6060 1.00 758 37 0.2080 0.2010 REMARK 3 10 2.6060 - 2.4730 1.00 800 46 0.1960 0.2370 REMARK 3 11 2.4730 - 2.3580 1.00 822 48 0.1770 0.1860 REMARK 3 12 2.3580 - 2.2580 1.00 877 44 0.1940 0.2240 REMARK 3 13 2.2580 - 2.1700 1.00 903 55 0.1880 0.2170 REMARK 3 14 2.1700 - 2.0910 1.00 919 43 0.1730 0.1950 REMARK 3 15 2.0910 - 2.0200 1.00 996 49 0.1820 0.1730 REMARK 3 16 2.0200 - 1.9560 1.00 1000 61 0.1870 0.2360 REMARK 3 17 1.9560 - 1.8980 1.00 1001 70 0.1950 0.2320 REMARK 3 18 1.8980 - 1.8450 1.00 1073 38 0.2200 0.1690 REMARK 3 19 1.8450 - 1.7950 1.00 1086 61 0.2410 0.2620 REMARK 3 20 1.7950 - 1.7500 1.00 1116 59 0.2940 0.4270 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 SOLVENT RADIUS : 1.20 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70100 REMARK 3 B22 (A**2) : 0.70100 REMARK 3 B33 (A**2) : -1.40200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6ZGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 - 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20190315 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 46.331 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.10 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 67.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 23.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BIPYRAMID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE; 2M TRIS PH 8.5; 100 REMARK 280 MM, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 60.44150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.08100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.08100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.22075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.08100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.08100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.66225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.08100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.08100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.22075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.08100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.08100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.66225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 60.44150 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6730 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 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 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 376 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 381 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 SER A 64 REMARK 465 ASN A 65 REMARK 465 LYS A 66 REMARK 465 VAL A 67 REMARK 465 GLY A 68 REMARK 465 THR A 69 REMARK 465 LEU A 70 REMARK 465 GLN A 71 REMARK 465 ALA A 72 REMARK 465 GLN A 73 REMARK 465 VAL A 74 REMARK 465 GLU A 75 REMARK 465 ALA A 76 REMARK 465 THR A 77 REMARK 465 GLN A 78 REMARK 465 LYS A 79 REMARK 465 GLN A 80 REMARK 465 LYS A 81 REMARK 465 ALA A 82 REMARK 465 GLN A 83 REMARK 465 PRO A 84 REMARK 465 ILE A 85 REMARK 465 ASP A 86 REMARK 465 ALA A 87 REMARK 465 ASN A 88 REMARK 465 ARG A 89 REMARK 465 LYS A 90 REMARK 465 TYR A 91 REMARK 465 LYS A 134 REMARK 465 ALA A 135 REMARK 465 GLN A 136 REMARK 465 GLY A 137 REMARK 465 GLN A 138 REMARK 465 GLN A 169 REMARK 465 HIS A 170 REMARK 465 ASP A 171 REMARK 465 LYS A 172 REMARK 465 ASP A 173 REMARK 465 THR A 174 REMARK 465 GLU A 175 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 381 DISTANCE = 7.50 ANGSTROMS DBREF 6ZGN A 64 204 UNP Q70CA4 Q70CA4_STRTR 64 204 SEQRES 1 A 141 SER ASN LYS VAL GLY THR LEU GLN ALA GLN VAL GLU ALA SEQRES 2 A 141 THR GLN LYS GLN LYS ALA GLN PRO ILE ASP ALA ASN ARG SEQRES 3 A 141 LYS TYR ASP TYR LYS LEU GLN TYR TYR LEU ASN ASP TYR SEQRES 4 A 141 VAL TYR ALA TYR PHE THR LEU PRO GLN GLU GLY ASP LYS SEQRES 5 A 141 GLN GLN ALA GLN VAL GLU HIS LEU ASN SER PHE TYR ASN SEQRES 6 A 141 PHE VAL PRO ASP VAL LYS ALA GLN GLY GLN VAL ARG ASN SEQRES 7 A 141 PRO SER THR LEU LEU ASP SER GLN LEU VAL THR VAL GLU SEQRES 8 A 141 GLY LYS VAL ALA THR TYR LYS VAL LYS TYR LYS GLU MET SEQRES 9 A 141 ILE GLN HIS ASP LYS ASP THR GLU GLU LYS GLU LEU VAL SEQRES 10 A 141 THR GLY PHE ASN ILE PRO PHE ASP GLU LYS GLU GLY LYS SEQRES 11 A 141 TYR TYR VAL SER GLY LEU PRO TRP PHE SER ALA FORMUL 2 HOH *81(H2 O) HELIX 1 AA1 ASP A 92 PHE A 107 1 16 HELIX 2 AA2 GLU A 112 SER A 125 1 14 SHEET 1 AA1 4 THR A 144 GLU A 154 0 SHEET 2 AA1 4 VAL A 157 LYS A 165 -1 O LYS A 163 N ASP A 147 SHEET 3 AA1 4 LEU A 179 LYS A 190 -1 O LEU A 179 N TYR A 164 SHEET 4 AA1 4 LYS A 193 VAL A 196 -1 O TYR A 195 N ASP A 188 SHEET 1 AA2 4 THR A 144 GLU A 154 0 SHEET 2 AA2 4 VAL A 157 LYS A 165 -1 O LYS A 163 N ASP A 147 SHEET 3 AA2 4 LEU A 179 LYS A 190 -1 O LEU A 179 N TYR A 164 SHEET 4 AA2 4 TRP A 201 SER A 203 -1 O TRP A 201 N ASN A 184 CRYST1 50.162 50.162 120.883 90.00 90.00 90.00 P 41 21 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 0.019935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008272 0.00000