HEADER PROTEIN BINDING 31-DEC-10 3Q6B TITLE THE HIGH-RESOLUTION AND NEW FORM CRYSTAL STRUCTURE OF BAMA POTRA4-5 TITLE 2 FROM E.COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN ASSEMBLY COMPLEX, YAET PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POTRA45 DOMAIN (UNP RESIDUES 266-420); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: ECDH1_3426, YAET; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS POTRA FOLD, INSERTION OF OUTER MEMBRANE PROTEINS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Z.Q.GAO,H.ZHANG,Y.H.DONG REVDAT 2 01-NOV-23 3Q6B 1 SEQADV REVDAT 1 10-AUG-11 3Q6B 0 JRNL AUTH H.ZHANG,Z.Q.GAO,H.F.HOU,J.H.XU,L.F.LI,X.D.SU,Y.H.DONG JRNL TITL HIGH-RESOLUTION STRUCTURE OF A NEW CRYSTAL FORM OF BAMA JRNL TITL 2 POTRA4-5 FROM ESCHERICHIA COLI. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 734 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 21795783 JRNL DOI 10.1107/S1744309111014254 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 25465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1294 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 25.7975 - 3.1124 0.97 2898 158 0.1682 0.1886 REMARK 3 2 3.1124 - 2.4711 1.00 2916 160 0.1523 0.1895 REMARK 3 3 2.4711 - 2.1589 1.00 2872 149 0.1329 0.1880 REMARK 3 4 2.1589 - 1.9616 0.99 2858 178 0.1241 0.1815 REMARK 3 5 1.9616 - 1.8210 0.97 2775 158 0.1154 0.1648 REMARK 3 6 1.8210 - 1.7137 0.94 2726 137 0.1119 0.1653 REMARK 3 7 1.7137 - 1.6279 0.92 2672 122 0.1269 0.2005 REMARK 3 8 1.6279 - 1.5570 0.88 2541 129 0.1435 0.2055 REMARK 3 9 1.5570 - 1.5000 0.70 2008 103 0.2007 0.3068 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 44.23 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28620 REMARK 3 B22 (A**2) : -1.58070 REMARK 3 B33 (A**2) : 1.29450 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.22290 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 : 0.005 1306 REMARK 3 ANGLE : 0.938 1766 REMARK 3 CHIRALITY : 0.057 190 REMARK 3 PLANARITY : 0.003 236 REMARK 3 DIHEDRAL : 12.614 525 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 3Q6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-10 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 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: PDB ENTRY 3OG5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE, 0.1M SODIUM REMARK 280 CACODYLATE PH 6.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 68.76500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.50250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.76500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.50250 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: 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 MET A 232 REMARK 465 GLY A 233 REMARK 465 SER A 234 REMARK 465 SER A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 SER A 242 REMARK 465 SER A 243 REMARK 465 GLY A 244 REMARK 465 GLU A 245 REMARK 465 ASN A 246 REMARK 465 LEU A 247 REMARK 465 TYR A 248 REMARK 465 PHE A 249 REMARK 465 GLU A 250 REMARK 465 GLY A 251 REMARK 465 SER A 252 REMARK 465 HIS A 253 REMARK 465 MET A 254 REMARK 465 ALA A 255 REMARK 465 SER A 256 REMARK 465 MET A 257 REMARK 465 THR A 258 REMARK 465 GLY A 259 REMARK 465 GLY A 260 REMARK 465 GLN A 261 REMARK 465 GLN A 262 REMARK 465 MET A 263 REMARK 465 GLY A 264 REMARK 465 ARG A 265 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 28 O HOH A 140 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OG5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BAMA POTRA45 TANDEM DBREF 3Q6B A 266 420 UNP C9QRL1 C9QRL1_ECOD1 266 420 SEQADV 3Q6B MET A 232 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLY A 233 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B SER A 234 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B SER A 235 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 236 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 237 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 238 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 239 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 240 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 241 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B SER A 242 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B SER A 243 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLY A 244 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLU A 245 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B ASN A 246 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B LEU A 247 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B TYR A 248 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B PHE A 249 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLU A 250 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLY A 251 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B SER A 252 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B HIS A 253 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B MET A 254 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B ALA A 255 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B SER A 256 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B MET A 257 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B THR A 258 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLY A 259 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLY A 260 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLN A 261 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLN A 262 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B MET A 263 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B GLY A 264 UNP C9QRL1 EXPRESSION TAG SEQADV 3Q6B ARG A 265 UNP C9QRL1 EXPRESSION TAG SEQRES 1 A 189 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 189 GLU ASN LEU TYR PHE GLU GLY SER HIS MET ALA SER MET SEQRES 3 A 189 THR GLY GLY GLN GLN MET GLY ARG TYR LYS LEU SER GLY SEQRES 4 A 189 VAL GLU VAL SER GLY ASN LEU ALA GLY HIS SER ALA GLU SEQRES 5 A 189 ILE GLU GLN LEU THR LYS ILE GLU PRO GLY GLU LEU TYR SEQRES 6 A 189 ASN GLY THR LYS VAL THR LYS MET GLU ASP ASP ILE LYS SEQRES 7 A 189 LYS LEU LEU GLY ARG TYR GLY TYR ALA TYR PRO ARG VAL SEQRES 8 A 189 GLN SER MET PRO GLU ILE ASN ASP ALA ASP LYS THR VAL SEQRES 9 A 189 LYS LEU ARG VAL ASN VAL ASP ALA GLY ASN ARG PHE TYR SEQRES 10 A 189 VAL ARG LYS ILE ARG PHE GLU GLY ASN ASP THR SER LYS SEQRES 11 A 189 ASP ALA VAL LEU ARG ARG GLU MET ARG GLN MET GLU GLY SEQRES 12 A 189 ALA TRP LEU GLY SER ASP LEU VAL ASP GLN GLY LYS GLU SEQRES 13 A 189 ARG LEU ASN ARG LEU GLY PHE PHE GLU THR VAL ASP THR SEQRES 14 A 189 ASP THR GLN ARG VAL PRO GLY SER PRO ASP GLN VAL ASP SEQRES 15 A 189 VAL VAL TYR LYS VAL LYS GLU FORMUL 2 HOH *141(H2 O) HELIX 1 1 HIS A 280 THR A 288 1 9 HELIX 2 2 ASN A 297 ARG A 314 1 18 HELIX 3 3 LYS A 361 ARG A 367 1 7 HELIX 4 4 GLY A 378 GLY A 393 1 16 SHEET 1 A 3 LYS A 267 ASN A 276 0 SHEET 2 A 3 THR A 334 ASP A 342 1 O VAL A 335 N LYS A 267 SHEET 3 A 3 ARG A 321 ASN A 329 -1 N ASN A 329 O THR A 334 SHEET 1 B 3 TYR A 348 GLU A 355 0 SHEET 2 B 3 SER A 408 LYS A 419 1 O TYR A 416 N ARG A 353 SHEET 3 B 3 THR A 397 VAL A 405 -1 N ASP A 401 O VAL A 415 CRYST1 137.530 39.005 32.561 90.00 101.00 90.00 C 1 2 1 4 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 0.007271 0.000000 0.001413 0.00000 SCALE2 0.000000 0.025638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031286 0.00000