HEADER PROTEIN BINDING 26-SEP-18 6MKX TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE- TITLE 2 BINDING PROTEIN (LAO) R77A MUTANT FROM SALMONELLA TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE/ARGININE/ORNITHINE-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LAO-BINDING PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / SOURCE 3 ATCC 700720); SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: ARGT, STM2355; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21-AI; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET12B KEYWDS PERIPLASMIC BINDING PROTEIN, LAO, THERMODYNAMICS, PROTEIN LIGAND KEYWDS 2 COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.ROMERO-ROMERO,R.VERGARA,G.ESPINOZA-PEREZ,A.RODRIGUEZ-ROMERO REVDAT 3 11-OCT-23 6MKX 1 REMARK REVDAT 2 26-FEB-20 6MKX 1 JRNL REVDAT 1 07-AUG-19 6MKX 0 JRNL AUTH R.VERGARA,S.ROMERO-ROMERO,I.VELAZQUEZ-LOPEZ, JRNL AUTH 2 G.ESPINOZA-PEREZ,A.RODRIGUEZ-HERNANDEZ,N.O.PULIDO, JRNL AUTH 3 A.SOSA-PEINADO,A.RODRIGUEZ-ROMERO,D.A.FERNANDEZ-VELASCO JRNL TITL THE INTERPLAY OF PROTEIN-LIGAND AND WATER-MEDIATED JRNL TITL 2 INTERACTIONS SHAPE AFFINITY AND SELECTIVITY IN THE LAO JRNL TITL 3 BINDING PROTEIN. JRNL REF FEBS J. V. 287 763 2020 JRNL REFN ISSN 1742-464X JRNL PMID 31348608 JRNL DOI 10.1111/FEBS.15019 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11054 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) : 0.191 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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 43.0886 - 4.3680 1.00 1537 153 0.1757 0.2087 REMARK 3 2 4.3680 - 3.4675 1.00 1448 144 0.1563 0.2153 REMARK 3 3 3.4675 - 3.0293 1.00 1443 144 0.1837 0.2651 REMARK 3 4 3.0293 - 2.7524 1.00 1417 140 0.2256 0.2685 REMARK 3 5 2.7524 - 2.5551 1.00 1406 140 0.2217 0.2697 REMARK 3 6 2.5551 - 2.4045 1.00 1412 141 0.2227 0.3605 REMARK 3 7 2.4045 - 2.2841 0.99 1391 138 0.2399 0.2985 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.90 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 : 0.010 1851 REMARK 3 ANGLE : 1.061 2518 REMARK 3 CHIRALITY : 0.057 283 REMARK 3 PLANARITY : 0.007 331 REMARK 3 DIHEDRAL : 5.766 1503 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 6MKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000237132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX HF REMARK 200 OPTICS : OSMIC VARIMAX CU-HF REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11886 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.284 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 : 7.200 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: 2LAO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M REMARK 280 SODIUM CACODYLATE TRIHYDRATE 30% W/V POLYETHYLENE GLYCOL 8,000, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.50050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.08100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.08100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.50050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.37500 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 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 4 CG CD OE1 NE2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 GLN A 219 CG CD OE1 NE2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 229 CG CD CE NZ 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 THR A 12 39.98 -79.26 REMARK 500 TYR A 14 57.99 -142.03 REMARK 500 SER A 69 48.80 -157.31 REMARK 500 SER A 70 50.03 39.63 REMARK 500 PHE A 169 -52.22 -135.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 420 DISTANCE = 8.01 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6MKU RELATED DB: PDB REMARK 900 RELATED ID: 6MKW RELATED DB: PDB DBREF 6MKX A 1 238 UNP P02911 ARGT_SALTY 23 260 SEQADV 6MKX ALA A 77 UNP P02911 ARG 99 ENGINEERED MUTATION SEQRES 1 A 238 ALA LEU PRO GLN THR VAL ARG ILE GLY THR ASP THR THR SEQRES 2 A 238 TYR ALA PRO PHE SER SER LYS ASP ALA LYS GLY GLU PHE SEQRES 3 A 238 ILE GLY PHE ASP ILE ASP LEU GLY ASN GLU MET CYS LYS SEQRES 4 A 238 ARG MET GLN VAL LYS CYS THR TRP VAL ALA SER ASP PHE SEQRES 5 A 238 ASP ALA LEU ILE PRO SER LEU LYS ALA LYS LYS ILE ASP SEQRES 6 A 238 ALA ILE ILE SER SER LEU SER ILE THR ASP LYS ALA GLN SEQRES 7 A 238 GLN GLU ILE ALA PHE SER ASP LYS LEU TYR ALA ALA ASP SEQRES 8 A 238 SER ARG LEU ILE ALA ALA LYS GLY SER PRO ILE GLN PRO SEQRES 9 A 238 THR LEU GLU SER LEU LYS GLY LYS HIS VAL GLY VAL LEU SEQRES 10 A 238 GLN GLY SER THR GLN GLU ALA TYR ALA ASN ASP ASN TRP SEQRES 11 A 238 ARG THR LYS GLY VAL ASP VAL VAL ALA TYR ALA ASN GLN SEQRES 12 A 238 ASP LEU ILE TYR SER ASP LEU THR ALA GLY ARG LEU ASP SEQRES 13 A 238 ALA ALA LEU GLN ASP GLU VAL ALA ALA SER GLU GLY PHE SEQRES 14 A 238 LEU LYS GLN PRO ALA GLY LYS GLU TYR ALA PHE ALA GLY SEQRES 15 A 238 PRO SER VAL LYS ASP LYS LYS TYR PHE GLY ASP GLY THR SEQRES 16 A 238 GLY VAL GLY LEU ARG LYS ASP ASP THR GLU LEU LYS ALA SEQRES 17 A 238 ALA PHE ASP LYS ALA LEU THR GLU LEU ARG GLN ASP GLY SEQRES 18 A 238 THR TYR ASP LYS MET ALA LYS LYS TYR PHE ASP PHE ASN SEQRES 19 A 238 VAL TYR GLY ASP FORMUL 2 HOH *120(H2 O) HELIX 1 AA1 GLY A 28 GLN A 42 1 15 HELIX 2 AA2 ASP A 51 ASP A 53 5 3 HELIX 3 AA3 ALA A 54 ALA A 61 1 8 HELIX 4 AA4 THR A 74 ILE A 81 1 8 HELIX 5 AA5 THR A 105 LYS A 110 1 6 HELIX 6 AA6 SER A 120 TRP A 130 1 11 HELIX 7 AA7 ARG A 131 GLY A 134 5 4 HELIX 8 AA8 ASN A 142 GLY A 153 1 12 HELIX 9 AA9 GLU A 162 PHE A 169 1 8 HELIX 10 AB1 GLN A 172 LYS A 176 5 5 HELIX 11 AB2 ASP A 187 GLY A 192 1 6 HELIX 12 AB3 ASP A 203 ASP A 220 1 18 HELIX 13 AB4 GLY A 221 LYS A 229 1 9 SHEET 1 AA1 3 LYS A 44 ALA A 49 0 SHEET 2 AA1 3 THR A 5 THR A 10 1 N ILE A 8 O THR A 46 SHEET 3 AA1 3 ALA A 66 ILE A 67 1 O ALA A 66 N GLY A 9 SHEET 1 AA2 3 THR A 13 TYR A 14 0 SHEET 2 AA2 3 SER A 18 LYS A 20 -1 O SER A 18 N TYR A 14 SHEET 3 AA2 3 PHE A 26 ILE A 27 -1 O ILE A 27 N SER A 19 SHEET 1 AA3 2 ALA A 82 PHE A 83 0 SHEET 2 AA3 2 GLY A 198 LEU A 199 -1 O LEU A 199 N ALA A 82 SHEET 1 AA4 5 ASP A 136 TYR A 140 0 SHEET 2 AA4 5 HIS A 113 LEU A 117 1 N VAL A 114 O VAL A 138 SHEET 3 AA4 5 ALA A 157 ASP A 161 1 O ALA A 157 N GLY A 115 SHEET 4 AA4 5 SER A 92 ALA A 97 -1 N ARG A 93 O GLN A 160 SHEET 5 AA4 5 TYR A 178 PHE A 180 -1 O ALA A 179 N ALA A 96 SSBOND 1 CYS A 38 CYS A 45 1555 1555 2.03 CISPEP 1 ALA A 15 PRO A 16 0 4.11 CRYST1 35.001 76.750 86.162 90.00 90.00 90.00 P 21 21 21 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 0.028571 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011606 0.00000