HEADER PROTEIN TRANSPORT 23-NOV-09 3KSN TITLE CRYSTAL STRUCTURE OF THE LIPOPROTEIN LOCALIZATION FACTOR, LOLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 22-203; COMPND 5 SYNONYM: P20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B0891, JW0874, LOLA, LPLA, YZZV; 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: PDEST17 KEYWDS LIPOPROTEIN CARRIER, CHAPERONE, TRANSPORT, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.AHMADPOUR,M.GLOYD,A.GUARNE,G.STEWART,R.PATHANIA,E.D.BROWN REVDAT 3 06-SEP-23 3KSN 1 SEQADV REVDAT 2 16-NOV-11 3KSN 1 VERSN HETATM REVDAT 1 06-OCT-10 3KSN 0 JRNL AUTH F.AHMADPOUR,M.GLOYD,A.GUARNE,G.STEWART,R.PATHANIA,E.D.BROWN JRNL TITL CRYSTAL STRUCTURE OF THE LIPOPROTEIN LOCALIZATION FACTOR, JRNL TITL 2 LOLA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_159) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20534 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1052 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 31.5832 - 3.2973 0.98 2529 136 0.1783 0.1967 REMARK 3 2 3.2973 - 2.6176 1.00 2471 122 0.2037 0.2803 REMARK 3 3 2.6176 - 2.2868 1.00 2457 131 0.1965 0.2375 REMARK 3 4 2.2868 - 2.0778 1.00 2436 115 0.1873 0.2446 REMARK 3 5 2.0778 - 1.9289 1.00 2413 130 0.1741 0.2704 REMARK 3 6 1.9289 - 1.8152 0.99 2370 146 0.1899 0.2776 REMARK 3 7 1.8152 - 1.7243 1.00 2389 138 0.1781 0.3084 REMARK 3 8 1.7243 - 1.6500 0.99 2417 134 0.2136 0.2714 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 : 0.40 REMARK 3 B_SOL : 60.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61850 REMARK 3 B22 (A**2) : 0.61850 REMARK 3 B33 (A**2) : -1.23710 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.006 1441 REMARK 3 ANGLE : 1.063 1955 REMARK 3 CHIRALITY : 0.067 209 REMARK 3 PLANARITY : 0.004 260 REMARK 3 DIHEDRAL : 18.946 516 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 3KSN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20611 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 39.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 REMARK 200 R SYM FOR SHELL (I) : 0.49100 REMARK 200 FOR SHELL : 4.470 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: 1AU8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1000, 20% PEG 8000, 0.1 M REMARK 280 SODIUM ACETATE, DEHYDRATED OVER 1M AMMONIUM SULFATE, PH 4.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.83400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.41700 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.41700 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.83400 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 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 210 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 217 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 249 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 0 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 GLY A 29 REMARK 465 ALA A 30 REMARK 465 ALA A 31 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 102 CG CD OE1 NE2 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 45 -15.37 76.01 REMARK 500 LYS A 155 -67.04 -96.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 119 SER A 120 -132.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UA8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LIPOPROTEIN LOCALIZATION FACTOR, LOLA DBREF 3KSN A 1 182 UNP P61316 LOLA_ECOLI 22 203 SEQADV 3KSN GLY A 0 UNP P61316 EXPRESSION TAG SEQRES 1 A 183 GLY ASP ALA ALA SER ASP LEU LYS SER ARG LEU ASP LYS SEQRES 2 A 183 VAL SER SER PHE HIS ALA SER PHE THR GLN LYS VAL THR SEQRES 3 A 183 ASP GLY SER GLY ALA ALA VAL GLN GLU GLY GLN GLY ASP SEQRES 4 A 183 LEU TRP VAL LYS ARG PRO ASN LEU PHE ASN TRP HIS MET SEQRES 5 A 183 THR GLN PRO ASP GLU SER ILE LEU VAL SER ASP GLY LYS SEQRES 6 A 183 THR LEU TRP PHE TYR ASN PRO PHE VAL GLU GLN ALA THR SEQRES 7 A 183 ALA THR TRP LEU LYS ASP ALA THR GLY ASN THR PRO PHE SEQRES 8 A 183 MET LEU ILE ALA ARG ASN GLN SER SER ASP TRP GLN GLN SEQRES 9 A 183 TYR ASN ILE LYS GLN ASN GLY ASP ASP PHE VAL LEU THR SEQRES 10 A 183 PRO LYS ALA SER ASN GLY ASN LEU LYS GLN PHE THR ILE SEQRES 11 A 183 ASN VAL GLY ARG ASP GLY THR ILE HIS GLN PHE SER ALA SEQRES 12 A 183 VAL GLU GLN ASP ASP GLN ARG SER SER TYR GLN LEU LYS SEQRES 13 A 183 SER GLN GLN ASN GLY ALA VAL ASP ALA ALA LYS PHE THR SEQRES 14 A 183 PHE THR PRO PRO GLN GLY VAL THR VAL ASP ASP GLN ARG SEQRES 15 A 183 LYS FORMUL 2 HOH *79(H2 O) HELIX 1 1 ASP A 1 LYS A 12 1 12 HELIX 2 2 PRO A 71 VAL A 73 5 3 HELIX 3 3 LYS A 82 ALA A 84 5 3 HELIX 4 4 THR A 88 ASN A 96 1 9 HELIX 5 5 GLN A 97 GLN A 102 1 6 HELIX 6 6 ASP A 163 THR A 168 5 6 SHEET 1 A12 TYR A 104 ASN A 109 0 SHEET 2 A12 ASP A 112 PRO A 117 -1 O THR A 116 N ASN A 105 SHEET 3 A12 LEU A 124 VAL A 131 -1 O PHE A 127 N LEU A 115 SHEET 4 A12 ILE A 137 GLU A 144 -1 O GLN A 139 N ASN A 130 SHEET 5 A12 ARG A 149 ASN A 159 -1 O TYR A 152 N PHE A 140 SHEET 6 A12 SER A 15 THR A 25 -1 N SER A 19 O LYS A 155 SHEET 7 A12 GLU A 34 LYS A 42 -1 O GLY A 35 N GLN A 22 SHEET 8 A12 LEU A 46 GLN A 53 -1 O HIS A 50 N ASP A 38 SHEET 9 A12 SER A 57 SER A 61 -1 O SER A 61 N PHE A 47 SHEET 10 A12 THR A 65 ASN A 70 -1 O TYR A 69 N ILE A 58 SHEET 11 A12 GLN A 75 TRP A 80 -1 O THR A 79 N LEU A 66 SHEET 12 A12 THR A 176 ASP A 179 1 O ASP A 178 N ALA A 76 CISPEP 1 ARG A 43 PRO A 44 0 -4.50 CISPEP 2 GLN A 53 PRO A 54 0 -3.67 CRYST1 60.357 60.357 79.251 90.00 90.00 120.00 P 32 2 1 6 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 0.016568 0.009566 0.000000 0.00000 SCALE2 0.000000 0.019131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012618 0.00000