HEADER PROTEIN TRANSPORT/PROTEIN TRANSPORT 03-MAR-15 2N01 TITLE NMR STRUCTURE OF VIRB9 C-TERMINAL DOMAIN IN COMPLEX WITH VIRB7 N- TITLE 2 TERMINAL DOMAIN FROM XANTHOMONAS CITRI'S T4SS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRB7 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 24-46); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VIRB9 PROTEIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 154-255); COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: XANTHOMONAS AXONOPODIS PV. CITRI; SOURCE 4 ORGANISM_TAXID: 190486; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: XANTHOMONAS AXONOPODIS PV. CITRI; SOURCE 7 ORGANISM_TAXID: 190486; SOURCE 8 STRAIN: 306; SOURCE 9 GENE: VIRB9, XAC2620, XAC2622; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS T4SS, LIPOPROTEIN, PROTEIN-PEPTIDE COMPLEX, VIRB9, VIRB7, PROTEIN KEYWDS 2 TRANSPORT-PROTEIN TRANSPORT COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.C.OLIVEIRA,D.P.SOUZA,R.K.SALINAS,H.WIENK,R.BOELENS,S.C.FARAH REVDAT 5 20-NOV-24 2N01 1 REMARK REVDAT 4 01-MAY-24 2N01 1 REMARK SEQADV REVDAT 3 19-OCT-16 2N01 1 JRNL REVDAT 2 12-OCT-16 2N01 1 JRNL REVDAT 1 09-SEP-15 2N01 0 JRNL AUTH L.C.OLIVEIRA,D.P.SOUZA,G.U.OKA,F.D.LIMA,R.J.OLIVEIRA, JRNL AUTH 2 D.C.FAVARO,H.WIENK,R.BOELENS,C.S.FARAH,R.K.SALINAS JRNL TITL VIRB7 AND VIRB9 INTERACTIONS ARE REQUIRED FOR THE ASSEMBLY JRNL TITL 2 AND ANTIBACTERIAL ACTIVITY OF A TYPE IV SECRETION SYSTEM. JRNL REF STRUCTURE V. 24 1707 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27594685 JRNL DOI 10.1016/J.STR.2016.07.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0, CNS REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RECALCULATION USING RECOORD SCRIPTS, REMARK 3 WATER REFINEMENT USING RECOORD SCRIPTS REMARK 4 REMARK 4 2N01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000104250. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 0.07 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.500 MM [U-99% 13C; U-99% 15N] REMARK 210 XAC_VIRB9CT, 1 MM XAC_VIRB7NT, REMARK 210 20 MM [U-100% 2H] SODIUM ACETATE, REMARK 210 50 MM SODIUM CHLORIDE, 1 % REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 2D 1H-1H REMARK 210 NOESY; 3D CBCA(CO)NH; 3D C(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D H(CCO)NH; REMARK 210 3D HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D CCH TOCSY; 3D REMARK 210 HNCACB; 3D 15N, 13C CNH-NOESY; REMARK 210 2D 13C15N FILTERED NOE; 2D 13C, REMARK 210 15N FILTERED TOCSY; 3D REMARK 210 HBCBCGCDHD; 3D 15N-EDITED NOESY; REMARK 210 3D 13C-EDITED NOESY; 3D HN(CO)CA; REMARK 210 3D HN(CA)CO; 3D HBCBCGCDCEHE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS, NMRPIPE, CCPNMR ANALYSIS REMARK 210 2.4.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, WATER REMARK 210 REFINEMENT IN CARTESIAN SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 ACE A 23 REMARK 465 NH2 A 47 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 PRO A 26 31.65 -82.37 REMARK 500 1 HIS A 39 90.89 -59.28 REMARK 500 1 GLU A 42 -39.54 -167.66 REMARK 500 1 THR A 45 -58.60 -153.88 REMARK 500 1 HIS B 152 -55.58 73.19 REMARK 500 1 LEU B 158 -167.33 58.89 REMARK 500 1 LYS B 188 -42.11 -144.81 REMARK 500 1 VAL B 220 -167.76 40.39 REMARK 500 2 PRO A 28 98.42 -62.32 REMARK 500 2 HIS A 39 -95.40 69.80 REMARK 500 2 PHE A 40 9.41 -152.77 REMARK 500 2 ASP A 41 -161.14 -112.91 REMARK 500 2 GLU A 42 16.85 -143.43 REMARK 500 2 THR A 45 74.39 40.24 REMARK 500 2 MET B 153 -93.35 60.52 REMARK 500 2 LEU B 158 75.66 60.18 REMARK 500 2 ASP B 160 -159.27 172.26 REMARK 500 2 LYS B 188 -42.48 -146.50 REMARK 500 2 ASN B 203 27.87 -79.95 REMARK 500 2 VAL B 220 -163.35 35.02 REMARK 500 3 TRP A 34 100.32 -35.91 REMARK 500 3 ASP A 41 -69.82 -152.62 REMARK 500 3 ASN B 154 98.57 77.19 REMARK 500 3 ALA B 155 -175.75 68.30 REMARK 500 3 LYS B 159 -165.31 -106.13 REMARK 500 3 LYS B 188 -45.08 -141.36 REMARK 500 3 ASN B 203 36.01 -87.76 REMARK 500 3 VAL B 220 -170.59 38.70 REMARK 500 4 LYS A 25 83.38 -151.26 REMARK 500 4 ASP A 29 -60.53 68.24 REMARK 500 4 HIS A 39 -86.68 73.65 REMARK 500 4 ASP A 41 -99.00 -107.97 REMARK 500 4 ALA A 43 98.46 65.20 REMARK 500 4 LYS B 159 75.34 32.03 REMARK 500 4 ARG B 162 -138.92 -110.07 REMARK 500 4 LYS B 188 -39.26 -142.34 REMARK 500 4 ASN B 203 39.76 -87.43 REMARK 500 4 VAL B 220 -165.13 35.79 REMARK 500 5 ASP A 29 166.07 66.30 REMARK 500 5 PHE A 40 121.14 72.47 REMARK 500 5 ASP A 41 -153.15 -120.15 REMARK 500 5 SER B 151 -83.29 -98.72 REMARK 500 5 LYS B 188 -34.12 -155.18 REMARK 500 5 ASP B 195 54.51 -95.07 REMARK 500 5 THR B 201 -2.51 71.26 REMARK 500 5 ASN B 203 48.27 -83.07 REMARK 500 5 VAL B 220 -169.94 37.97 REMARK 500 6 LYS A 25 100.27 72.17 REMARK 500 6 ASN A 38 94.08 -68.23 REMARK 500 6 HIS A 39 -81.27 70.25 REMARK 500 REMARK 500 THIS ENTRY HAS 177 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG B 198 0.07 SIDE CHAIN REMARK 500 4 ARG B 210 0.07 SIDE CHAIN REMARK 500 7 ARG B 251 0.10 SIDE CHAIN REMARK 500 19 ARG B 251 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L4W RELATED DB: PDB REMARK 900 NMR STRUCTURE OF VIRB7 FROM XANTHOMONAS CITRI REMARK 900 RELATED ID: 25512 RELATED DB: BMRB DBREF 2N01 A 24 46 UNP Q8PJB3 Q8PJB3_XANAC 24 46 DBREF 2N01 B 154 255 UNP Q8PJB5 Q8PJB5_XANAC 154 255 SEQADV 2N01 ACE A 23 UNP Q8PJB3 ACETYLATION SEQADV 2N01 NH2 A 47 UNP Q8PJB3 AMIDATION SEQADV 2N01 GLY B 150 UNP Q8PJB5 EXPRESSION TAG SEQADV 2N01 SER B 151 UNP Q8PJB5 EXPRESSION TAG SEQADV 2N01 HIS B 152 UNP Q8PJB5 EXPRESSION TAG SEQADV 2N01 MET B 153 UNP Q8PJB5 EXPRESSION TAG SEQRES 1 A 25 ACE THR LYS PRO ALA PRO ASP PHE GLY GLY ARG TRP LYS SEQRES 2 A 25 HIS VAL ASN HIS PHE ASP GLU ALA PRO THR GLU NH2 SEQRES 1 B 106 GLY SER HIS MET ASN ALA LYS ILE LEU LYS ASP ARG ARG SEQRES 2 B 106 TYR TYR TYR ASP TYR ASP TYR ALA THR ARG THR LYS LYS SEQRES 3 B 106 SER TRP LEU ILE PRO SER ARG VAL TYR ASP ASP GLY LYS SEQRES 4 B 106 PHE THR TYR ILE ASN MET ASP LEU THR ARG PHE PRO THR SEQRES 5 B 106 GLY ASN PHE PRO ALA VAL PHE ALA ARG GLU LYS GLU HIS SEQRES 6 B 106 ALA GLU ASP PHE LEU VAL ASN THR THR VAL GLU GLY ASN SEQRES 7 B 106 THR LEU ILE VAL HIS GLY THR TYR PRO PHE LEU VAL VAL SEQRES 8 B 106 ARG HIS GLY ASP ASN VAL VAL GLY LEU ARG ARG ASN LYS SEQRES 9 B 106 GLN LYS HELIX 1 1 ASP B 195 PHE B 199 5 5 SHEET 1 A 5 LYS A 35 HIS A 36 0 SHEET 2 A 5 TYR B 167 THR B 171 -1 O TYR B 169 N LYS A 35 SHEET 3 A 5 ASN B 245 ARG B 251 -1 O GLY B 248 N ALA B 170 SHEET 4 A 5 PHE B 237 HIS B 242 -1 N VAL B 240 O VAL B 247 SHEET 5 A 5 ALA B 206 ARG B 210 -1 N PHE B 208 O VAL B 239 SHEET 1 B 5 TYR B 163 TYR B 164 0 SHEET 2 B 5 ARG B 182 ASP B 186 -1 O ASP B 185 N TYR B 164 SHEET 3 B 5 PHE B 189 ASN B 193 -1 O TYR B 191 N TYR B 184 SHEET 4 B 5 THR B 228 HIS B 232 -1 O VAL B 231 N THR B 190 SHEET 5 B 5 ASN B 221 GLU B 225 -1 N THR B 223 O ILE B 230 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1