HEADER TRANSPORT PROTEIN 24-JUL-14 4UU4 TITLE CRYSTAL STRUCTURE OF LPTH, THE LPTA HOMOLOGOUS PERIPLASMIC COMPONENT TITLE 2 OF THE CONSERVED LIPOPOLYSACCHARIDE TRANSPORT DEVICE FROM PSEUDOMONAS TITLE 3 AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC LIPOPOLYSACCHARIDE TRANSPORT PROTEIN LPTH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15PREP4 KEYWDS TRANSPORT PROTEIN, LPTH, LPTA, LPS EXPDTA X-RAY DIFFRACTION AUTHOR M.BOLLATI,R.VILLA,L.J.GOURLAY,A.BARBIROLI,G.DEHO,M.BENEDET,A.POLISSI, AUTHOR 2 A.MARTORANA,P.SPERANDEO,M.BOLOGNESI,M.NARDINI REVDAT 3 10-JAN-24 4UU4 1 REMARK REVDAT 2 03-JUN-15 4UU4 1 JRNL REVDAT 1 25-MAR-15 4UU4 0 JRNL AUTH M.BOLLATI,R.VILLA,L.J.GOURLAY,M.BENEDET,G.DEHO,A.POLISSI, JRNL AUTH 2 A.BARBIROLI,A.M.MARTORANA,P.SPERANDEO,M.BOLOGNESI,N.MARCO JRNL TITL CRYSTAL STRUCTURE OF LPTH, THE PERIPLASMIC COMPONENT OF THE JRNL TITL 2 LIPOPOLYSACCHARIDE TRANSPORT MACHINERY FROM PSEUDOMONAS JRNL TITL 3 AERUGINOSA. JRNL REF FEBS J. V. 282 1980 2015 JRNL REFN ISSN 1742-464X JRNL PMID 25735820 JRNL DOI 10.1111/FEBS.13254 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 4331 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 344 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 43.0257 - 3.4654 0.99 3526 170 0.2291 0.3061 REMARK 3 2 3.4654 - 2.7507 1.00 3581 174 0.2466 0.2788 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.070 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) : 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 : 0.005 1120 REMARK 3 ANGLE : 0.911 1518 REMARK 3 CHIRALITY : 0.070 177 REMARK 3 PLANARITY : 0.005 201 REMARK 3 DIHEDRAL : 18.339 429 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 4UU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1290061326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97241 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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 2R19 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% 1,4-BUTANEDIOL, 0.1 M HEPES (PH REMARK 280 7.5), 0.2 M NACL. 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 73.33000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.99500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.66500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.99500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.66500 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 73.33000 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 1 REMARK 465 ARG A 2 REMARK 465 PHE A 3 REMARK 465 VAL A 4 REMARK 465 ASN A 5 REMARK 465 THR A 6 REMARK 465 LEU A 7 REMARK 465 PRO A 8 REMARK 465 LEU A 9 REMARK 465 ILE A 10 REMARK 465 PHE A 11 REMARK 465 GLY A 12 REMARK 465 LEU A 13 REMARK 465 THR A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 SER A 20 REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 LEU A 23 REMARK 465 ALA A 24 REMARK 465 LEU A 25 REMARK 465 ASP A 78 REMARK 465 ILE A 79 REMARK 465 LYS A 171 REMARK 465 LYS A 172 REMARK 465 LYS A 173 REMARK 465 ALA A 174 REMARK 465 GLN A 175 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 NZ LYS A 94 O ASP A 98 1.42 REMARK 500 CE LYS A 94 O ASP A 98 2.09 REMARK 500 NZ LYS A 94 O ALA A 96 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 76 CB - CA - C ANGL. DEV. = -16.9 DEGREES 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 ARG A 29 -33.15 -143.01 REMARK 500 ASN A 76 -2.20 85.70 REMARK 500 ASP A 98 -166.78 -73.00 REMARK 500 LYS A 99 59.62 -94.12 REMARK 500 ASP A 122 81.06 52.84 REMARK 500 GLN A 123 34.03 82.18 REMARK 500 GLN A 143 -61.12 -91.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 4UU4 A 1 175 UNP Q9HVV7 Q9HVV7_PSEAE 1 175 SEQRES 1 A 175 MET ARG PHE VAL ASN THR LEU PRO LEU ILE PHE GLY LEU SEQRES 2 A 175 THR ALA ALA LEU GLY SER SER MET ALA LEU ALA LEU PRO SEQRES 3 A 175 SER ASP ARG GLU GLN PRO ILE ARG VAL GLN ALA ASP SER SEQRES 4 A 175 ALA GLU LEU ASP ASP LYS GLN GLY VAL ALA VAL TYR ARG SEQRES 5 A 175 GLY ASP VAL VAL VAL THR GLN GLY SER THR LYS LEU THR SEQRES 6 A 175 GLY ASN THR VAL THR LEU LYS GLN ASP LYS ASN GLY ASP SEQRES 7 A 175 ILE GLU VAL VAL THR SER VAL GLY LYS PRO ALA TYR TYR SEQRES 8 A 175 GLU GLN LYS PRO ALA PRO ASP LYS ASP VAL THR LYS ALA SEQRES 9 A 175 TYR GLY LEU THR ILE GLN TYR PHE VAL THR GLN ASN ARG SEQRES 10 A 175 VAL VAL LEU ILE ASP GLN ALA LYS VAL ILE GLN GLU GLY SEQRES 11 A 175 ASN THR PHE GLU GLY GLU LYS ILE VAL TYR ASP THR GLN SEQRES 12 A 175 ARG GLN ILE VAL ASN ALA GLY ARG ALA THR GLY SER GLN SEQRES 13 A 175 VAL THR SER PRO ARG PRO ARG ILE ASP MET VAL ILE GLN SEQRES 14 A 175 PRO LYS LYS LYS ALA GLN FORMUL 2 HOH *32(H2 O) SHEET 1 AA 2 ARG A 34 GLN A 36 0 SHEET 2 AA 2 VAL A 48 GLN A 59 1 O VAL A 56 N GLN A 36 SHEET 1 AB 2 SER A 39 ASP A 43 0 SHEET 2 AB 2 VAL A 48 GLN A 59 -1 O VAL A 48 N ASP A 43 SHEET 1 AC 2 VAL A 147 GLY A 150 0 SHEET 2 AC 2 ASN A 131 ASP A 141 -1 N GLU A 136 O GLY A 150 SHEET 1 AD 2 ASP A 165 VAL A 167 0 SHEET 2 AD 2 ASN A 131 ASP A 141 -1 O THR A 132 N VAL A 167 CISPEP 1 LYS A 87 PRO A 88 0 -5.97 CRYST1 45.000 45.000 146.660 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 0.022222 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022222 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006818 0.00000