Header list of 1l1m.pdb file
Complete list - t 27 2 Bytes
HEADER TRANSCRIPTION REGULATOR/DNA 19-FEB-02 1L1M
TITLE SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN
TITLE 2 COMPLEXED TO ITS NATURAL OPERATOR O1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP
COMPND 3 *AP*AP*TP*TP*T)-3';
COMPND 4 CHAIN: C;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: LAC OPERATOR O1; THIS IS THE WILD-TYPE OPERATOR
COMPND 7 SEQUENCE OF THE LAC OPERON IN E. COLI.;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP
COMPND 10 *AP*AP*TP*TP*C)-3';
COMPND 11 CHAIN: D;
COMPND 12 ENGINEERED: YES;
COMPND 13 OTHER_DETAILS: LAC OPERATOR O1; THIS IS THE WILD-TYPE OPERATOR
COMPND 14 SEQUENCE OF THE LAC OPERON IN E. COLI.;
COMPND 15 MOL_ID: 3;
COMPND 16 MOLECULE: LACTOSE OPERON REPRESSOR;
COMPND 17 CHAIN: A, B;
COMPND 18 FRAGMENT: N-TERMINAL DNA-BINDING DOMAIN, RESIDUES 1-62;
COMPND 19 ENGINEERED: YES;
COMPND 20 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 7 ORGANISM_TAXID: 562;
SOURCE 8 GENE: LACI;
SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 11 EXPRESSION_SYSTEM_STRAIN: DH9;
SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PGP1-2,PET-HP62
KEYWDS TRANSCRIPTION REGULATION, LAC OPERON, LAC REPRESSOR, NATURAL LAC
KEYWDS 2 OPERATOR, ASYMMETRIC DNA-BINDING, HTH, TRANSCRIPTION REGULATOR-DNA
KEYWDS 3 COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR C.G.KALODIMOS,A.M.J.J.BONVIN,R.K.SALINAS,R.WECHSELBERGER,R.BOELENS,
AUTHOR 2 R.KAPTEIN
REVDAT 4 27-OCT-21 1L1M 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1L1M 1 VERSN
REVDAT 2 01-APR-03 1L1M 1 JRNL
REVDAT 1 26-JUN-02 1L1M 0
JRNL AUTH C.G.KALODIMOS,A.M.BONVIN,R.K.SALINAS,R.WECHSELBERGER,
JRNL AUTH 2 R.BOELENS,R.KAPTEIN
JRNL TITL PLASTICITY IN PROTEIN-DNA RECOGNITION: LAC REPRESSOR
JRNL TITL 2 INTERACTS WITH ITS NATURAL OPERATOR 01 THROUGH ALTERNATIVE
JRNL TITL 3 CONFORMATIONS OF ITS DNA-BINDING DOMAIN.
JRNL REF EMBO J. V. 21 2866 2002
JRNL REFN ISSN 0261-4189
JRNL PMID 12065400
JRNL DOI 10.1093/EMBOJ/CDF318
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.G.KALODIMOS,G.FOLKERS,R.BOELENS,R.KAPTEIN
REMARK 1 TITL STRONG DNA BINDING BY COVALENTLY LINKED DIMERIC LAC
REMARK 1 TITL 2 HEADPIECE: EVIDENCE FOR THE CRUCIAL ROLE OF THE HINGE
REMARK 1 TITL 3 HELICES
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 98 6039 2001
REMARK 1 REFN ISSN 0027-8424
REMARK 1 DOI 10.1073/PNAS.101129898
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.1, CNS 1.1
REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF THE COMPLEX WAS
REMARK 3 CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LAC
REMARK 3 HP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE
REMARK 3 50 BEST STRUCTURES WERE SELECTED AND DOCKED ONTO THE NATURAL LAC
REMARK 3 OPERATOR B-DNA USING SIMULATED ANNEALING. DISTANCE AND PLANARITY
REMARK 3 RESTRAINTS FOR THE DNA WERE INCORPORATED IN ORDER TO KEEP DNA
REMARK 3 CLOSE TO B-DNA BUT ALLOWING A BEND NECESSARY TO ACCOMMODATE THE
REMARK 3 TWO HEADPIECE MOLECULES ON THE DNA.
REMARK 4
REMARK 4 1L1M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-02.
REMARK 100 THE DEPOSITION ID IS D_1000015560.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 315
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 10MM KPI, 20MM KCL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2MM LAC-HP62-V52C U-15N,13C,
REMARK 210 10MM KPI, 20MM KCL, 90% H2O, 10%
REMARK 210 D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 1.0, NMRVIEW 5.0.4, CNS
REMARK 210 1.1
REMARK 210 METHOD USED : SIMULATED ANNEALING FOLLOWED BY
REMARK 210 RESTRAINED MDR
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HOMO- AND
REMARK 210 HETERONUCLEARNUCLEAR TECHNIQUES.
REMARK 210 13C-15N LABELED PROTEIN WAS USED AND UNLABELED NUCLEOTIDE.
REMARK 210 IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO OBTAIN
REMARK 210 ADDITIONAL ASSIGNMENTS AND TO ASSIGN INTER-MOLECULAR NOES. FOR
REMARK 210 FURTHER DETAILS SEE THE REFERENCE DESCRIBING THE STRUCTURES.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B
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 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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 H21 DG C 10 O2 DC D 14 1.53
REMARK 500 H21 DG C 13 O2 DC D 11 1.58
REMARK 500 H61 DA C 19 O4 DT D 5 1.60
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 16 DG C 13 O4' - C1' - N9 ANGL. DEV. = 2.0 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 1 VAL A 15 -166.54 -123.56
REMARK 500 1 GLN A 26 64.59 62.49
REMARK 500 1 ALA A 27 -84.22 -121.75
REMARK 500 1 ASN A 46 64.98 63.63
REMARK 500 1 LYS A 59 104.62 69.62
REMARK 500 1 ASN B 25 -73.26 -123.52
REMARK 500 1 PRO B 49 138.81 -38.67
REMARK 500 1 ASN B 50 97.13 -62.59
REMARK 500 1 LYS B 59 65.90 -153.77
REMARK 500 2 ALA A 27 -137.15 -95.15
REMARK 500 2 ASN A 46 63.02 68.34
REMARK 500 2 ASN B 25 -75.08 -98.20
REMARK 500 2 ALA B 27 95.20 -50.77
REMARK 500 2 SER B 31 41.26 -86.77
REMARK 500 2 ALA B 32 -61.45 67.84
REMARK 500 2 ASN B 46 65.73 67.36
REMARK 500 2 ASN B 50 95.73 -58.17
REMARK 500 2 LYS B 59 89.50 62.83
REMARK 500 3 VAL A 15 -166.15 -124.12
REMARK 500 3 ALA A 27 -141.58 -94.14
REMARK 500 3 ASN A 46 64.83 66.65
REMARK 500 3 LYS A 59 -138.83 39.81
REMARK 500 3 LYS B 2 70.56 62.09
REMARK 500 3 ASN B 25 -74.91 -64.29
REMARK 500 3 GLN B 26 16.33 -146.35
REMARK 500 3 TYR B 47 108.77 -59.27
REMARK 500 3 PRO B 49 119.13 -30.44
REMARK 500 3 ASN B 50 88.34 -67.19
REMARK 500 3 ALA B 57 -80.29 -69.64
REMARK 500 3 LYS B 59 120.81 70.40
REMARK 500 4 ALA A 27 30.17 -85.89
REMARK 500 4 SER A 28 -172.82 60.59
REMARK 500 4 ASN A 46 63.50 67.75
REMARK 500 4 ASN B 25 -72.18 -128.45
REMARK 500 4 PRO B 49 122.51 -28.21
REMARK 500 4 ALA B 57 44.12 -73.61
REMARK 500 4 SER B 61 41.04 -88.73
REMARK 500 5 ALA A 27 -148.58 -103.02
REMARK 500 5 ASN A 46 67.18 64.51
REMARK 500 5 GLN A 60 90.94 -66.60
REMARK 500 5 ASN B 25 -73.74 -72.55
REMARK 500 5 GLN B 26 41.06 -167.23
REMARK 500 5 ALA B 27 -117.15 64.61
REMARK 500 5 SER B 28 120.23 58.94
REMARK 500 5 TYR B 47 108.99 -52.66
REMARK 500 5 PRO B 49 130.49 -30.86
REMARK 500 5 LEU B 56 -70.60 -70.63
REMARK 500 6 LYS A 2 81.71 -159.93
REMARK 500 6 GLN A 26 -53.38 -129.10
REMARK 500 6 SER A 31 -89.14 -74.07
REMARK 500
REMARK 500 THIS ENTRY HAS 203 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1L1M A 1 62 UNP P03023 LACI_ECOLI 1 62
DBREF 1L1M B 1 62 UNP P03023 LACI_ECOLI 1 62
DBREF 1L1M C 1 23 PDB 1L1M 1L1M 1 23
DBREF 1L1M D 1 23 PDB 1L1M 1L1M 1 23
SEQADV 1L1M CYS A 52 UNP P03023 VAL 52 ENGINEERED MUTATION
SEQADV 1L1M CYS B 52 UNP P03023 VAL 52 ENGINEERED MUTATION
SEQRES 1 C 23 DG DA DA DT DT DG DT DG DA DG DC DG DG
SEQRES 2 C 23 DA DT DA DA DC DA DA DT DT DT
SEQRES 1 D 23 DA DA DA DT DT DG DT DT DA DT DC DC DG
SEQRES 2 D 23 DC DT DC DA DC DA DA DT DT DC
SEQRES 1 A 62 MET LYS PRO VAL THR LEU TYR ASP VAL ALA GLU TYR ALA
SEQRES 2 A 62 GLY VAL SER TYR GLN THR VAL SER ARG VAL VAL ASN GLN
SEQRES 3 A 62 ALA SER HIS VAL SER ALA LYS THR ARG GLU LYS VAL GLU
SEQRES 4 A 62 ALA ALA MET ALA GLU LEU ASN TYR ILE PRO ASN ARG CYS
SEQRES 5 A 62 ALA GLN GLN LEU ALA GLY LYS GLN SER LEU
SEQRES 1 B 62 MET LYS PRO VAL THR LEU TYR ASP VAL ALA GLU TYR ALA
SEQRES 2 B 62 GLY VAL SER TYR GLN THR VAL SER ARG VAL VAL ASN GLN
SEQRES 3 B 62 ALA SER HIS VAL SER ALA LYS THR ARG GLU LYS VAL GLU
SEQRES 4 B 62 ALA ALA MET ALA GLU LEU ASN TYR ILE PRO ASN ARG CYS
SEQRES 5 B 62 ALA GLN GLN LEU ALA GLY LYS GLN SER LEU
HELIX 1 1 THR A 5 GLY A 14 1 10
HELIX 2 2 SER A 16 GLN A 26 1 11
HELIX 3 3 SER A 31 LEU A 45 1 15
HELIX 4 4 ASN A 50 GLY A 58 1 9
HELIX 5 5 THR B 5 GLY B 14 1 10
HELIX 6 6 SER B 16 ASN B 25 1 10
HELIX 7 7 SER B 31 LEU B 45 1 15
HELIX 8 8 ASN B 50 GLY B 58 1 9
SSBOND 1 CYS A 52 CYS B 52 1555 1555 2.03
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - t 27 2 Bytes