HEADER AMINO ACID TRANSPORT 06-OCT-93 1LAG
TITLE STRUCTURAL BASES FOR MULTIPLE LIGAND SPECIFICITY OF THE PERIPLASMIC
TITLE 2 LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE, ARGININE, ORNITHINE-BINDING PROTEIN;
COMPND 3 CHAIN: E;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM;
SOURCE 3 ORGANISM_TAXID: 602
KEYWDS AMINO ACID TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR S.-H.KIM,B.-H.OH
REVDAT 3 29-NOV-17 1LAG 1 HELIX
REVDAT 2 24-FEB-09 1LAG 1 VERSN
REVDAT 1 10-JUL-95 1LAG 0
JRNL AUTH B.H.OH,G.F.AMES,S.H.KIM
JRNL TITL STRUCTURAL BASIS FOR MULTIPLE LIGAND SPECIFICITY OF THE
JRNL TITL 2 PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN.
JRNL REF J.BIOL.CHEM. V. 269 26323 1994
JRNL REFN ISSN 0021-9258
JRNL PMID 7929349
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH B.-H.OH,J.PANDIT,C.-H.KANG,K.NIKAIDO,S.GOKCEN,G.F.-L.AMES,
REMARK 1 AUTH 2 S.-H.KIM
REMARK 1 TITL THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-,
REMARK 1 TITL 2 ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A
REMARK 1 TITL 3 LIGAND
REMARK 1 REF J.BIOL.CHEM. V. 268 11348 1993
REMARK 1 REFN ISSN 0021-9258
REMARK 2
REMARK 2 RESOLUTION. 2.06 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.162
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1814
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 11
REMARK 3 SOLVENT ATOMS : 134
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.013
REMARK 3 BOND ANGLES (DEGREES) : 2.700
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.220
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1LAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000174630.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
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 : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.03
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 18.74500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.82500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.09500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.82500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.74500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.09500
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: E
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 E 4 CG CD OE1 NE2
REMARK 470 LYS E 110 CG CD CE NZ
REMARK 470 LYS E 188 CG CD CE NZ
REMARK 470 LYS E 189 CG CD CE NZ
REMARK 470 LYS E 228 CG CD CE NZ
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 TRP E 47 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES
REMARK 500 TRP E 47 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500 TRP E 130 CD1 - CG - CD2 ANGL. DEV. = 5.3 DEGREES
REMARK 500 TRP E 130 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES
REMARK 500 ARG E 218 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 TYR E 230 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES
REMARK 500 ASN E 234 CB - CG - ND2 ANGL. DEV. = 15.0 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 THR E 12 22.28 -75.97
REMARK 500 SER E 69 48.25 -153.52
REMARK 500 PRO E 104 60.82 -69.91
REMARK 500 PHE E 169 -50.55 -141.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HIS E 240
DBREF 1LAG E 1 238 UNP P02911 ARGT_SALTY 23 260
SEQADV 1LAG ILE E 102 UNP P02911 VAL 124 CONFLICT
SEQRES 1 E 238 ALA LEU PRO GLN THR VAL ARG ILE GLY THR ASP THR THR
SEQRES 2 E 238 TYR ALA PRO PHE SER SER LYS ASP ALA LYS GLY GLU PHE
SEQRES 3 E 238 ILE GLY PHE ASP ILE ASP LEU GLY ASN GLU MET CYS LYS
SEQRES 4 E 238 ARG MET GLN VAL LYS CYS THR TRP VAL ALA SER ASP PHE
SEQRES 5 E 238 ASP ALA LEU ILE PRO SER LEU LYS ALA LYS LYS ILE ASP
SEQRES 6 E 238 ALA ILE ILE SER SER LEU SER ILE THR ASP LYS ARG GLN
SEQRES 7 E 238 GLN GLU ILE ALA PHE SER ASP LYS LEU TYR ALA ALA ASP
SEQRES 8 E 238 SER ARG LEU ILE ALA ALA LYS GLY SER PRO ILE GLN PRO
SEQRES 9 E 238 THR LEU GLU SER LEU LYS GLY LYS HIS VAL GLY VAL LEU
SEQRES 10 E 238 GLN GLY SER THR GLN GLU ALA TYR ALA ASN ASP ASN TRP
SEQRES 11 E 238 ARG THR LYS GLY VAL ASP VAL VAL ALA TYR ALA ASN GLN
SEQRES 12 E 238 ASP LEU ILE TYR SER ASP LEU THR ALA GLY ARG LEU ASP
SEQRES 13 E 238 ALA ALA LEU GLN ASP GLU VAL ALA ALA SER GLU GLY PHE
SEQRES 14 E 238 LEU LYS GLN PRO ALA GLY LYS GLU TYR ALA PHE ALA GLY
SEQRES 15 E 238 PRO SER VAL LYS ASP LYS LYS TYR PHE GLY ASP GLY THR
SEQRES 16 E 238 GLY VAL GLY LEU ARG LYS ASP ASP THR GLU LEU LYS ALA
SEQRES 17 E 238 ALA PHE ASP LYS ALA LEU THR GLU LEU ARG GLN ASP GLY
SEQRES 18 E 238 THR TYR ASP LYS MET ALA LYS LYS TYR PHE ASP PHE ASN
SEQRES 19 E 238 VAL TYR GLY ASP
HET HIS E 240 11
HETNAM HIS HISTIDINE
FORMUL 2 HIS C6 H10 N3 O2 1+
FORMUL 3 HOH *134(H2 O)
HELIX 1 A PHE E 29 MET E 41 1 13
HELIX 2 B LEU E 55 LYS E 60 1 6
HELIX 3 C ASP E 75 GLU E 80 1 6
HELIX 4 D LEU E 106 LEU E 109 1 4
HELIX 5 E THR E 121 ASN E 129 1 9
HELIX 6 F GLN E 143 THR E 151 1 9
HELIX 7 G GLU E 162 GLY E 168 1 7
HELIX 8 H LYS E 188 PHE E 191 1 4
HELIX 9 I THR E 204 GLN E 219 1 16
HELIX 10 J THR E 222 LYS E 228 1 7
SHEET 1 S1 5 LYS E 44 ALA E 49 0
SHEET 2 S1 5 THR E 5 THR E 10 1
SHEET 3 S1 5 ALA E 66 ILE E 67 1
SHEET 4 S1 5 VAL E 197 LEU E 199 -1
SHEET 5 S1 5 ALA E 82 SER E 84 1
SHEET 1 S2 5 ASP E 136 TYR E 140 0
SHEET 2 S2 5 HIS E 113 LEU E 117 1
SHEET 3 S2 5 ALA E 157 ASP E 161 1
SHEET 4 S2 5 SER E 92 ALA E 97 -1
SHEET 5 S2 5 TYR E 178 ALA E 181 1
SSBOND 1 CYS E 38 CYS E 45 1555 1555 2.38
CISPEP 1 ALA E 15 PRO E 16 0 2.96
SITE 1 AC1 12 TYR E 14 PHE E 52 SER E 69 SER E 70
SITE 2 AC1 12 LEU E 71 SER E 72 ARG E 77 LEU E 117
SITE 3 AC1 12 SER E 120 THR E 121 GLN E 122 ASP E 161
CRYST1 37.490 58.190 117.650 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 0.026674 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017185 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008500 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
