HEADER MEMBRANE PROTEIN 26-JUN-17 5WAM TITLE STRUCTURE OF BAME FROM NEISSERIA GONORRHOEAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAME; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE (STRAIN ATCC 700825 / FA SOURCE 3 1090); SOURCE 4 ORGANISM_TAXID: 242231; SOURCE 5 STRAIN: ATCC 700825 / FA 1090; SOURCE 6 ATCC: 700825; SOURCE 7 GENE: BAME, NGO_1780; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET20BHT KEYWDS BETA-BARREL ASSEMBLY MACHINERY, BAM COMPLEX, LIPOPROTEIN, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.V.KOROTKOV,S.K.BUCHANAN,N.NOINAJ REVDAT 5 13-MAR-24 5WAM 1 LINK REVDAT 4 11-DEC-19 5WAM 1 REMARK REVDAT 3 07-FEB-18 5WAM 1 JRNL REVDAT 2 20-DEC-17 5WAM 1 JRNL REVDAT 1 06-DEC-17 5WAM 0 JRNL AUTH A.E.SIKORA,I.H.WIERZBICKI,R.A.ZIELKE,R.F.RYNER,K.V.KOROTKOV, JRNL AUTH 2 S.K.BUCHANAN,N.NOINAJ JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE ROLE OF BAMD AND JRNL TITL 2 BAME WITHIN THE BETA-BARREL ASSEMBLY MACHINERY IN NEISSERIA JRNL TITL 3 GONORRHOEAE. JRNL REF J. BIOL. CHEM. V. 293 1106 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29229778 JRNL DOI 10.1074/JBC.RA117.000437 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2722 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 10278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 522 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 43.1892 - 4.6784 0.93 2445 142 0.1778 0.1882 REMARK 3 2 4.6784 - 3.7140 0.95 2502 125 0.1462 0.1589 REMARK 3 3 3.7140 - 3.2447 0.95 2485 121 0.1818 0.2408 REMARK 3 4 3.2447 - 2.9481 0.97 2520 139 0.2330 0.3215 REMARK 3 5 2.9481 - 2.7368 0.95 2466 146 0.2443 0.3295 REMARK 3 6 2.7368 - 2.5755 0.96 2506 144 0.2644 0.3209 REMARK 3 7 2.5755 - 2.4500 0.97 2555 124 0.2880 0.3252 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.96 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 : 0.002 1615 REMARK 3 ANGLE : 0.450 2184 REMARK 3 CHIRALITY : 0.037 247 REMARK 3 PLANARITY : 0.002 286 REMARK 3 DIHEDRAL : 11.596 987 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 5WAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228678. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10309 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.79500 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 (%): 55.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M ZINC SULFATE, 0.1M MES PH 6.5, REMARK 280 25% PEG550MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 31.40200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.03750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.40200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.03750 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 244 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 18 REMARK 465 SER A 19 REMARK 465 VAL A 20 REMARK 465 GLU A 21 REMARK 465 ARG A 22 REMARK 465 GLY B 18 REMARK 465 SER B 19 REMARK 465 VAL B 20 REMARK 465 GLU B 21 REMARK 465 ARG B 22 REMARK 465 VAL B 23 REMARK 465 ASN B 121 REMARK 465 ALA B 122 REMARK 465 ASP B 123 REMARK 465 LYS B 124 REMARK 465 GLN B 125 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 ASN A 37 29.96 -140.76 REMARK 500 ARG B 66 36.96 -146.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 67 OD2 REMARK 620 2 HIS A 70 ND1 117.6 REMARK 620 3 GLU B 88 OE2 46.2 159.3 REMARK 620 4 ASP B 107 OD1 40.7 158.1 14.4 REMARK 620 5 ASP B 107 OD2 36.8 153.5 10.4 8.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WAQ RELATED DB: PDB DBREF 5WAM A 19 125 UNP Q5F5Y8 Q5F5Y8_NEIG1 19 125 DBREF 5WAM B 19 125 UNP Q5F5Y8 Q5F5Y8_NEIG1 19 125 SEQADV 5WAM GLY A 18 UNP Q5F5Y8 EXPRESSION TAG SEQADV 5WAM GLY B 18 UNP Q5F5Y8 EXPRESSION TAG SEQRES 1 A 108 GLY SER VAL GLU ARG VAL SER LEU PHE PRO SER TYR LYS SEQRES 2 A 108 LEU LYS ILE ILE GLN GLY ASN GLU LEU GLU PRO ARG ALA SEQRES 3 A 108 VAL ALA ALA LEU ARG PRO GLY MET THR LYS ASP GLN VAL SEQRES 4 A 108 LEU LEU LEU LEU GLY SER PRO ILE LEU ARG ASP ALA PHE SEQRES 5 A 108 HIS THR ASP ARG TRP ASP TYR THR PHE ASN THR SER ARG SEQRES 6 A 108 ASN GLY ILE ILE LYS GLU ARG SER ASN LEU THR VAL TYR SEQRES 7 A 108 PHE GLU ASN GLY VAL LEU VAL ARG THR GLU GLY ASP ALA SEQRES 8 A 108 LEU GLN ASN ALA ALA GLU ALA LEU ARG ALA LYS GLN ASN SEQRES 9 A 108 ALA ASP LYS GLN SEQRES 1 B 108 GLY SER VAL GLU ARG VAL SER LEU PHE PRO SER TYR LYS SEQRES 2 B 108 LEU LYS ILE ILE GLN GLY ASN GLU LEU GLU PRO ARG ALA SEQRES 3 B 108 VAL ALA ALA LEU ARG PRO GLY MET THR LYS ASP GLN VAL SEQRES 4 B 108 LEU LEU LEU LEU GLY SER PRO ILE LEU ARG ASP ALA PHE SEQRES 5 B 108 HIS THR ASP ARG TRP ASP TYR THR PHE ASN THR SER ARG SEQRES 6 B 108 ASN GLY ILE ILE LYS GLU ARG SER ASN LEU THR VAL TYR SEQRES 7 B 108 PHE GLU ASN GLY VAL LEU VAL ARG THR GLU GLY ASP ALA SEQRES 8 B 108 LEU GLN ASN ALA ALA GLU ALA LEU ARG ALA LYS GLN ASN SEQRES 9 B 108 ALA ASP LYS GLN HET ZN B 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *89(H2 O) HELIX 1 AA1 GLU A 40 ALA A 46 1 7 HELIX 2 AA2 THR A 52 GLY A 61 1 10 HELIX 3 AA3 ASP A 107 LYS A 124 1 18 HELIX 4 AA4 GLU B 40 ALA B 45 1 6 HELIX 5 AA5 THR B 52 GLY B 61 1 10 HELIX 6 AA6 GLY B 106 GLN B 120 1 15 SHEET 1 AA1 2 LYS A 30 GLY A 36 0 SHEET 2 AA1 2 SER B 28 ILE B 34 1 O ILE B 33 N ILE A 34 SHEET 1 AA2 3 ARG A 73 ARG A 82 0 SHEET 2 AA2 3 ILE A 85 GLU A 97 -1 O SER A 90 N PHE A 78 SHEET 3 AA2 3 VAL A 100 GLU A 105 -1 O GLU A 105 N THR A 93 SHEET 1 AA3 3 ARG B 73 ARG B 82 0 SHEET 2 AA3 3 ILE B 85 GLU B 97 -1 O LEU B 92 N TYR B 76 SHEET 3 AA3 3 VAL B 100 GLU B 105 -1 O GLU B 105 N THR B 93 LINK OD2 ASP A 67 ZN ZN B 201 1555 2555 1.94 LINK ND1 HIS A 70 ZN ZN B 201 1555 2555 2.00 LINK OE2 GLU B 88 ZN ZN B 201 1555 1555 1.87 LINK OD1 ASP B 107 ZN ZN B 201 1555 1555 2.35 LINK OD2 ASP B 107 ZN ZN B 201 1555 1555 2.50 SITE 1 AC1 4 ASP A 67 HIS A 70 GLU B 88 ASP B 107 CRYST1 62.804 86.075 49.919 90.00 90.00 90.00 P 21 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 0.015923 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020032 0.00000