HEADER MEMBRANE PROTEIN 26-JUN-17 5WAQ TITLE STRUCTURE OF BAMD FROM NEISSERIA GONORRHOEAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMD; COMPND 3 CHAIN: A; 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 GENE: BAMD, NGO_0277; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET20BHT KEYWDS BETA-BARREL ASSEMBLY MACHINERY, BAM COMPLEX, LIPOPROTEIN, TETRATRICO KEYWDS 2 PEPTIDE REPEAT, TPR DOMAIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.V.KOROTKOV,S.K.BUCHANAN,N.NOINAJ REVDAT 5 04-OCT-23 5WAQ 1 REMARK REVDAT 4 11-DEC-19 5WAQ 1 REMARK REVDAT 3 07-FEB-18 5WAQ 1 JRNL REVDAT 2 20-DEC-17 5WAQ 1 JRNL REVDAT 1 06-DEC-17 5WAQ 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1277 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 45.5558 - 5.2008 1.00 1409 157 0.1842 0.2625 REMARK 3 2 5.2008 - 4.1289 1.00 1301 144 0.2180 0.2217 REMARK 3 3 4.1289 - 3.6072 1.00 1276 141 0.2443 0.3056 REMARK 3 4 3.6072 - 3.2775 1.00 1275 142 0.2769 0.3458 REMARK 3 5 3.2775 - 3.0427 1.00 1253 139 0.3034 0.3675 REMARK 3 6 3.0427 - 2.8633 1.00 1262 141 0.3171 0.3270 REMARK 3 7 2.8633 - 2.7199 1.00 1250 139 0.3400 0.3339 REMARK 3 8 2.7199 - 2.6015 1.00 1224 135 0.3400 0.4027 REMARK 3 9 2.6015 - 2.5014 1.00 1246 139 0.3605 0.3567 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.47 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 1771 REMARK 3 ANGLE : 0.392 2393 REMARK 3 CHIRALITY : 0.032 252 REMARK 3 PLANARITY : 0.002 312 REMARK 3 DIHEDRAL : 19.755 1084 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 5WAQ 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_1000228686. 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 : 7.0 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 2.30000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2YHC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M LITHIUM CHLORIDE, 0.1M HEPES PH REMARK 280 7.0, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 83.19600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.20750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.20750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 124.79400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.20750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.20750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.59800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.20750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.20750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 124.79400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.20750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.20750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.59800 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 83.19600 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 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 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 17 REMARK 465 ALA A 18 REMARK 465 THR A 19 REMARK 465 GLN A 20 REMARK 465 GLY A 21 REMARK 465 THR A 22 REMARK 465 ALA A 23 REMARK 465 ASP A 24 REMARK 465 LYS A 25 REMARK 465 ASP A 26 REMARK 465 ALA A 27 REMARK 465 GLN A 28 REMARK 465 ILE A 29 REMARK 465 ASP A 123 REMARK 465 GLN A 124 REMARK 465 SER A 125 REMARK 465 PHE A 126 REMARK 465 LEU A 127 REMARK 465 ASN A 128 REMARK 465 LYS A 129 REMARK 465 LEU A 130 REMARK 465 ALA A 131 REMARK 465 SER A 132 REMARK 465 GLN A 133 REMARK 465 ASP A 134 REMARK 465 TRP A 135 REMARK 465 SER A 136 REMARK 465 ASP A 137 REMARK 465 ARG A 138 REMARK 465 ASP A 258 REMARK 465 ASP A 259 REMARK 465 MET A 260 REMARK 465 PRO A 261 REMARK 465 TRP A 262 REMARK 465 TRP A 263 REMARK 465 ARG A 264 REMARK 465 TYR A 265 REMARK 465 TRP A 266 REMARK 465 HIS A 267 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 GLN A 31 67.28 -162.83 REMARK 500 TRP A 33 -159.69 -119.57 REMARK 500 SER A 49 30.89 72.92 REMARK 500 GLU A 87 75.47 -100.29 REMARK 500 TYR A 208 53.18 -116.23 REMARK 500 ASP A 229 61.24 60.80 REMARK 500 LYS A 247 71.95 -107.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WAM RELATED DB: PDB DBREF 5WAQ A 18 267 UNP Q5F9W0 Q5F9W0_NEIG1 18 267 SEQADV 5WAQ GLY A 17 UNP Q5F9W0 EXPRESSION TAG SEQRES 1 A 251 GLY ALA THR GLN GLY THR ALA ASP LYS ASP ALA GLN ILE SEQRES 2 A 251 THR GLN ASP TRP SER VAL GLU LYS LEU TYR ALA GLU ALA SEQRES 3 A 251 GLN ASP GLU LEU ASN SER SER ASN TYR THR ARG ALA VAL SEQRES 4 A 251 LYS LEU TYR GLU ILE LEU GLU SER ARG PHE PRO THR SER SEQRES 5 A 251 ARG HIS ALA ARG GLN SER GLN LEU ASP THR ALA TYR ALA SEQRES 6 A 251 TYR TYR LYS ASP ASP GLU LYS ASP LYS ALA LEU ALA ALA SEQRES 7 A 251 ILE GLU ARG PHE ARG ARG LEU HIS PRO GLN HIS PRO ASN SEQRES 8 A 251 MET ASP TYR ALA LEU TYR LEU ARG GLY LEU VAL LEU PHE SEQRES 9 A 251 ASN GLU ASP GLN SER PHE LEU ASN LYS LEU ALA SER GLN SEQRES 10 A 251 ASP TRP SER ASP ARG ASP PRO LYS ALA ASN ARG GLU ALA SEQRES 11 A 251 TYR GLN ALA PHE ALA GLU LEU VAL GLN ARG PHE PRO ASN SEQRES 12 A 251 SER LYS TYR ALA ALA ASP ALA THR ALA ARG MET VAL LYS SEQRES 13 A 251 LEU VAL ASP ALA LEU GLY GLY ASN GLU MET SER VAL ALA SEQRES 14 A 251 ARG TYR TYR MET LYS ARG GLY ALA TYR ILE ALA ALA ALA SEQRES 15 A 251 ASN ARG ALA LYS LYS ILE ILE GLY SER TYR GLN ASN THR SEQRES 16 A 251 ARG TYR VAL GLU GLU SER LEU ALA ILE LEU GLU LEU ALA SEQRES 17 A 251 TYR LYS LYS LEU ASP LYS PRO GLN LEU ALA ALA ASP THR SEQRES 18 A 251 ARG ARG VAL LEU GLU THR ASN PHE PRO LYS SER PRO PHE SEQRES 19 A 251 LEU THR HIS ALA TRP GLN PRO ASP ASP MET PRO TRP TRP SEQRES 20 A 251 ARG TYR TRP HIS FORMUL 2 HOH *13(H2 O) HELIX 1 AA1 SER A 34 SER A 48 1 15 HELIX 2 AA2 ASN A 50 PHE A 65 1 16 HELIX 3 AA3 SER A 68 ASP A 85 1 18 HELIX 4 AA4 GLU A 87 HIS A 102 1 16 HELIX 5 AA5 ASN A 107 PHE A 120 1 14 HELIX 6 AA6 PRO A 140 PHE A 157 1 18 HELIX 7 AA7 TYR A 162 ARG A 191 1 30 HELIX 8 AA8 ALA A 193 TYR A 208 1 16 HELIX 9 AA9 TYR A 213 LEU A 228 1 16 HELIX 10 AB1 LYS A 230 PHE A 245 1 16 HELIX 11 AB2 SER A 248 HIS A 253 1 6 CRYST1 64.415 64.415 166.392 90.00 90.00 90.00 P 43 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 0.015524 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006010 0.00000