HEADER OXIDOREDUCTASE 09-OCT-08 2K9F TITLE STRUCTURAL FEATURES OF THE COMPLEX BETWEEN THE DSBD N-TERMINAL AND THE TITLE 2 PILB N-TERMINAL DOMAINS FROM NEISSERIA MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 34-176; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: SEQUENCE DATABASE RESIDUES 20-146; COMPND 10 SYNONYM: PROTEIN-DISULFIDE REDUCTASE, DISULFIDE REDUCTASE; COMPND 11 EC: 1.8.1.8; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP A; SOURCE 3 ORGANISM_TAXID: 65699; SOURCE 4 GENE: MSRAB, PILB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PETNTERPILBC70S; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B; SOURCE 10 ORGANISM_TAXID: 491; SOURCE 11 GENE: DSBD; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VECTOR: PETNDSBDC103S KEYWDS PROTEIN, DOCKING, THIOREDOXIN, IMMUNOGLOBULIN, DSBD, PILB, ELECTRON KEYWDS 2 TRANSPORT, MULTIFUNCTIONAL ENZYME, OXIDOREDUCTASE, REDOX-ACTIVE KEYWDS 3 CENTER, TRANSPORT, CYTOCHROME C-TYPE BIOGENESIS, INNER MEMBRANE, KEYWDS 4 MEMBRANE, NAD, TRANSMEMBRANE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.QUINTERNET,P.TSAN,L.SELME,C.JACOB,S.BOSCHI-MULLER,G.BRANLANT,M.CUNG REVDAT 4 16-OCT-24 2K9F 1 REMARK REVDAT 3 16-MAR-22 2K9F 1 REMARK SEQADV REVDAT 2 01-SEP-09 2K9F 1 JRNL REVDAT 1 19-MAY-09 2K9F 0 JRNL AUTH M.QUINTERNET,P.TSAN,L.SELME-ROUSSEL,C.JACOB,S.BOSCHI-MULLER, JRNL AUTH 2 G.BRANLANT,M.T.CUNG JRNL TITL FORMATION OF THE COMPLEX BETWEEN DSBD AND PILB N-TERMINAL JRNL TITL 2 DOMAINS FROM NEISSERIA MENINGITIDIS NECESSITATES AN JRNL TITL 3 ADAPTABILITY OF NDSBD. JRNL REF STRUCTURE V. 17 1024 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19604482 JRNL DOI 10.1016/J.STR.2009.05.011 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNSSOLVE 1.2, HADDOCK 2.0 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNSSOLVE), BONVIN AMJJ (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000100842. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM [U-13C; U-15N; U-2H] REMARK 210 NTERPILB, 0.75 MM NDSBD, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 0.75 MM [U-13C; U-15N; U-2H] REMARK 210 NDSBD, 0.75 MM NTERPILB, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 0.75 MM [U-100% 13C; U-100% REMARK 210 15N] NTERPILB, 0.75 MM NDSBD, 20 REMARK 210 MM POTASSIUM PHOSPHATE, 90% H2O/ REMARK 210 10% D2O; 0.75 MM [U-100% 13C; U- REMARK 210 100% 15N] NDSBD, 0.75 MM REMARK 210 NTERPILB, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HNHA; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK 2.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 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 HZ1 LYS A 30 OE1 GLU A 42 1.54 REMARK 500 HZ2 LYS B 60 OE1 GLU B 63 1.56 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 TYR A 86 84.06 66.97 REMARK 500 1 PRO A 87 37.96 -81.10 REMARK 500 1 LYS A 88 25.08 -150.02 REMARK 500 1 LEU B 3 -77.92 -142.41 REMARK 500 1 ASN B 6 -172.32 68.40 REMARK 500 1 ASP B 34 92.76 -69.21 REMARK 500 1 LEU B 52 43.58 -108.18 REMARK 500 1 GLN B 55 149.70 -171.63 REMARK 500 1 LYS B 60 122.18 70.57 REMARK 500 1 ARG B 71 122.89 -173.92 REMARK 500 1 HIS B 77 -35.75 -173.89 REMARK 500 1 ASN B 121 -15.94 -153.48 REMARK 500 2 TYR A 86 78.56 69.00 REMARK 500 2 ALA B 2 -60.41 -138.71 REMARK 500 2 ASN B 6 -159.34 62.39 REMARK 500 2 PRO B 49 -76.15 -76.11 REMARK 500 2 LEU B 52 57.24 -117.61 REMARK 500 2 LYS B 60 127.77 71.66 REMARK 500 2 HIS B 77 -39.88 179.25 REMARK 500 2 GLU B 104 21.69 -75.06 REMARK 500 3 TRP A 35 44.92 -90.89 REMARK 500 3 TYR A 86 73.81 71.09 REMARK 500 3 ASN A 104 61.44 60.58 REMARK 500 3 LEU B 3 -82.57 -85.37 REMARK 500 3 ASN B 6 -163.63 66.76 REMARK 500 3 LEU B 52 55.09 -90.16 REMARK 500 3 LYS B 60 127.90 71.82 REMARK 500 3 ARG B 71 117.91 -173.81 REMARK 500 3 HIS B 77 -36.07 -175.93 REMARK 500 4 LEU A 84 -161.82 -115.71 REMARK 500 4 ASN A 85 -168.89 -118.59 REMARK 500 4 TYR A 86 76.30 63.24 REMARK 500 4 LEU B 3 -73.09 -89.73 REMARK 500 4 ASN B 6 -170.36 65.68 REMARK 500 4 ALA B 22 -166.94 -119.69 REMARK 500 4 ASP B 34 91.79 -67.35 REMARK 500 4 LYS B 60 117.60 69.41 REMARK 500 4 ARG B 71 123.90 -171.09 REMARK 500 4 HIS B 77 -35.24 -159.88 REMARK 500 4 ALA B 79 101.57 -170.13 REMARK 500 5 VAL A 2 71.10 -119.88 REMARK 500 5 TYR A 86 82.11 66.60 REMARK 500 5 ASN A 104 70.82 65.79 REMARK 500 5 SER A 127 131.17 -170.57 REMARK 500 5 ARG A 138 -48.33 -133.69 REMARK 500 5 ALA B 2 -83.27 -74.65 REMARK 500 5 ASN B 6 -160.67 61.91 REMARK 500 5 PRO B 49 -76.93 -76.08 REMARK 500 5 ALA B 50 48.62 -105.57 REMARK 500 5 LYS B 60 136.86 72.72 REMARK 500 REMARK 500 THIS ENTRY HAS 111 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K0R RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE C103S MUTANT OF THE N-TERMINAL DOMAIN OF REMARK 900 DSBD FROM NEISSERIA MENINGITIDIS REMARK 900 RELATED ID: 2JZS RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE REDUCED FORM OF THE N-TERMINAL DOMAIN OF REMARK 900 PILB FROM N. MENINGITIDIS. REMARK 900 RELATED ID: 6709 RELATED DB: BMRB REMARK 900 NTERPILB (SEGID A) REMARK 900 RELATED ID: 15627 RELATED DB: BMRB REMARK 900 NDSBD (SEGID B) DBREF 2K9F A 2 144 UNP Q9JWM8 MSRAB_NEIMA 34 176 DBREF 2K9F B 2 128 UNP Q9JYM0 DSBD_NEIMB 20 146 SEQADV 2K9F MET A 1 UNP Q9JWM8 INITIATING METHIONINE SEQADV 2K9F MET B 1 UNP Q9JYM0 INITIATING METHIONINE SEQADV 2K9F ASN B 48 UNP Q9JYM0 ASP 66 CONFLICT SEQADV 2K9F SER B 102 UNP Q9JYM0 CYS 120 VARIANT SEQRES 1 A 144 MET VAL PRO HIS THR LEU SER THR LEU LYS THR ALA ASP SEQRES 2 A 144 ASN ARG PRO ALA SER VAL TYR LEU LYS LYS ASP LYS PRO SEQRES 3 A 144 THR LEU ILE LYS PHE TRP ALA SER TRP CYS PRO LEU CYS SEQRES 4 A 144 LEU SER GLU LEU GLY GLN THR GLU LYS TRP ALA GLN ASP SEQRES 5 A 144 ALA LYS PHE SER SER ALA ASN LEU ILE THR VAL ALA SER SEQRES 6 A 144 PRO GLY PHE LEU HIS GLU LYS LYS ASP GLY ASP PHE GLN SEQRES 7 A 144 LYS TRP TYR ALA GLY LEU ASN TYR PRO LYS LEU PRO VAL SEQRES 8 A 144 VAL THR ASP ASN GLY GLY THR ILE ALA GLN SER LEU ASN SEQRES 9 A 144 ILE SER VAL TYR PRO SER TRP ALA LEU ILE GLY LYS ASP SEQRES 10 A 144 GLY ASP VAL GLN ARG ILE VAL LYS GLY SER ILE ASN GLU SEQRES 11 A 144 ALA GLN ALA LEU ALA LEU ILE ARG ASP PRO ASN ALA ASP SEQRES 12 A 144 LEU SEQRES 1 B 128 MET ALA LEU ASP ALA ASN ASP LEU LEU PRO PRO GLU LYS SEQRES 2 B 128 ALA PHE VAL PRO GLU LEU ALA VAL ALA ASP ASP GLY VAL SEQRES 3 B 128 ASN VAL ARG PHE ARG ILE ALA ASP GLY TYR TYR MET TYR SEQRES 4 B 128 GLN ALA LYS ILE VAL GLY LYS THR ASN PRO ALA ASP LEU SEQRES 5 B 128 LEU GLY GLN PRO SER PHE SER LYS GLY GLU GLU LYS GLU SEQRES 6 B 128 ASP GLU PHE PHE GLY ARG GLN THR VAL TYR HIS HIS GLU SEQRES 7 B 128 ALA GLN VAL ALA PHE PRO TYR ALA LYS ALA VAL GLY GLU SEQRES 8 B 128 PRO TYR LYS LEU VAL LEU THR TYR GLN GLY SER ALA GLU SEQRES 9 B 128 ALA GLY VAL CYS TYR PRO PRO VAL ASP THR GLU PHE ASP SEQRES 10 B 128 ILE PHE GLY ASN GLY THR TYR HIS PRO GLN THR HELIX 1 1 VAL A 2 SER A 7 1 6 HELIX 2 2 PRO A 16 LEU A 21 5 6 HELIX 3 3 CYS A 36 GLN A 51 1 16 HELIX 4 4 LYS A 54 ALA A 58 5 5 HELIX 5 5 GLY A 67 GLU A 71 5 5 HELIX 6 6 ASP A 76 GLY A 83 1 8 HELIX 7 7 GLY A 97 LEU A 103 1 7 HELIX 8 8 ASN A 129 ASP A 139 1 11 HELIX 9 9 PRO B 10 ALA B 14 1 5 SHEET 1 A 6 LYS A 10 THR A 11 0 SHEET 2 A 6 VAL A 91 THR A 93 -1 O THR A 93 N LYS A 10 SHEET 3 A 6 ASN A 59 ALA A 64 1 N THR A 62 O VAL A 92 SHEET 4 A 6 THR A 27 PHE A 31 1 N LEU A 28 O ILE A 61 SHEET 5 A 6 SER A 110 ILE A 114 -1 O ILE A 114 N THR A 27 SHEET 6 A 6 VAL A 120 LYS A 125 -1 O ARG A 122 N LEU A 113 SHEET 1 B 4 PHE B 15 VAL B 21 0 SHEET 2 B 4 GLY B 25 ILE B 32 -1 O ARG B 31 N VAL B 16 SHEET 3 B 4 VAL B 81 PRO B 84 -1 O PHE B 83 N VAL B 26 SHEET 4 B 4 SER B 57 PHE B 58 -1 N SER B 57 O ALA B 82 SHEET 1 C 4 GLU B 62 GLU B 65 0 SHEET 2 C 4 ARG B 71 TYR B 75 -1 O GLN B 72 N LYS B 64 SHEET 3 C 4 TYR B 36 TYR B 39 -1 N MET B 38 O TYR B 75 SHEET 4 C 4 GLY B 101 ALA B 103 -1 O SER B 102 N TYR B 37 SHEET 1 D 3 VAL B 44 ASN B 48 0 SHEET 2 D 3 TYR B 93 TYR B 99 -1 O VAL B 96 N LYS B 46 SHEET 3 D 3 VAL B 112 ILE B 118 -1 O PHE B 116 N LEU B 95 SSBOND 1 CYS A 36 CYS B 108 1555 1555 2.03 CISPEP 1 TYR A 108 PRO A 109 1 -0.71 CISPEP 2 TYR A 108 PRO A 109 2 -0.90 CISPEP 3 TYR A 108 PRO A 109 3 -0.89 CISPEP 4 TYR A 108 PRO A 109 4 -1.04 CISPEP 5 TYR A 108 PRO A 109 5 -0.62 CISPEP 6 TYR A 108 PRO A 109 6 -1.31 CISPEP 7 TYR A 108 PRO A 109 7 -0.81 CISPEP 8 TYR A 108 PRO A 109 8 -0.87 CISPEP 9 TYR A 108 PRO A 109 9 -1.36 CISPEP 10 TYR A 108 PRO A 109 10 -1.94 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