Header list of 1rxr.pdb file
Complete list - r 14 2 Bytes
HEADER TRANSCRIPTION FACTOR 12-JUN-98 1RXR
TITLE HIGH RESOLUTION SOLUTION STRUCTURE OF THE RETINOID X RECEPTOR DNA
TITLE 2 BINDING DOMAIN, NMR, 20 STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR-ALPHA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, 130-212;
COMPND 5 SYNONYM: RXR-ALPHA;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 CELL_LINE: BL21;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A
KEYWDS TRANSCRIPTION FACTOR, NUCLEAR HORMONE RECEPTOR, ZINC-FINGER
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR S.M.A.HOLMBECK,M.P.FOSTER,D.R.CASIMIRO,D.S.SEM,H.J.DYSON,P.E.WRIGHT
REVDAT 3 14-MAR-18 1RXR 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1RXR 1 VERSN
REVDAT 1 11-NOV-98 1RXR 0
JRNL AUTH S.M.HOLMBECK,M.P.FOSTER,D.R.CASIMIRO,D.S.SEM,H.J.DYSON,
JRNL AUTH 2 P.E.WRIGHT
JRNL TITL HIGH-RESOLUTION SOLUTION STRUCTURE OF THE RETINOID X
JRNL TITL 2 RECEPTOR DNA-BINDING DOMAIN.
JRNL REF J.MOL.BIOL. V. 281 271 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9698548
JRNL DOI 10.1006/JMBI.1998.1908
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,
REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE
REMARK 4
REMARK 4 1RXR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000176268.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 6.6
REMARK 210 IONIC STRENGTH : 120
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : WATER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : CBCA(CO)NH; HBHA(CBCACO)NH;
REMARK 210 CBCANH; C(CO)NH-TOCSY; HCCH-COSY;
REMARK 210 HCCH-TOCSY; 13C-EDITED NOESY;
REMARK 210 15N-EDITED NOESY; 15N-EDITED
REMARK 210 TOCSY; HNHA; HNHB; HACAHB-COSY;
REMARK 210 13C-13CO; 13C-15N SPIN ECHO
REMARK 210 DIFFERENCE CT-HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX; DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : SYBYL TRIAD TRIAD, DIANA, AMBER
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED
REMARK 210 MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 83
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST RESTRAINT VIOLATIONS AND
REMARK 210 AMBER ENERGIES
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED RXR-DBD
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: MONOMERIC
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 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 4 CYS A 177 CA - CB - SG ANGL. DEV. = 7.5 DEGREES
REMARK 500 14 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.1 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 HIS A 133 70.89 -69.06
REMARK 500 1 ILE A 137 -73.56 -80.63
REMARK 500 1 ASN A 185 -8.87 -58.42
REMARK 500 1 LYS A 201 73.78 -69.90
REMARK 500 2 THR A 131 -60.75 71.97
REMARK 500 2 CYS A 177 99.18 -50.69
REMARK 500 2 CYS A 187 35.84 -150.87
REMARK 500 2 LYS A 201 85.42 -67.75
REMARK 500 2 GLN A 206 38.76 -80.28
REMARK 500 3 LEU A 167 94.28 -63.89
REMARK 500 3 ARG A 172 48.00 -75.68
REMARK 500 3 LYS A 201 85.62 -69.37
REMARK 500 4 HIS A 133 156.09 -47.38
REMARK 500 4 ARG A 172 46.76 -76.75
REMARK 500 4 ASP A 173 -109.06 -160.25
REMARK 500 4 CYS A 177 66.33 -67.91
REMARK 500 4 ARG A 182 63.20 -112.30
REMARK 500 4 LYS A 201 86.25 -70.00
REMARK 500 5 HIS A 133 -177.57 -60.14
REMARK 500 5 ASP A 173 -139.29 -156.12
REMARK 500 5 LYS A 201 79.68 -68.88
REMARK 500 6 ASP A 173 -135.11 -131.36
REMARK 500 6 ASN A 174 -158.22 -129.10
REMARK 500 6 LYS A 175 -4.96 -54.27
REMARK 500 6 GLN A 183 45.43 -71.55
REMARK 500 6 GLN A 188 -79.68 -42.34
REMARK 500 6 LYS A 201 84.27 -65.38
REMARK 500 7 THR A 131 -70.25 -60.93
REMARK 500 7 ASN A 174 -150.12 -86.28
REMARK 500 7 LYS A 175 -6.78 -54.44
REMARK 500 7 LYS A 201 84.61 -64.82
REMARK 500 8 THR A 131 -56.68 70.17
REMARK 500 8 ILE A 137 -78.90 -80.97
REMARK 500 8 ASP A 173 -127.11 -149.67
REMARK 500 8 LYS A 201 82.01 -66.23
REMARK 500 8 ARG A 211 69.09 -63.96
REMARK 500 9 CYS A 187 34.68 -154.14
REMARK 500 9 LYS A 201 82.89 -69.89
REMARK 500 9 GLN A 206 38.85 -90.14
REMARK 500 9 GLU A 207 -77.64 -84.38
REMARK 500 9 ARG A 209 43.95 -74.12
REMARK 500 10 ARG A 186 -38.47 -38.69
REMARK 500 10 CYS A 187 50.00 -79.14
REMARK 500 10 LYS A 201 86.96 -66.68
REMARK 500 10 ARG A 209 131.39 -38.96
REMARK 500 11 THR A 131 -69.50 70.54
REMARK 500 11 ASP A 173 -110.22 -99.98
REMARK 500 11 CYS A 177 72.14 -69.55
REMARK 500 11 ARG A 209 72.19 -106.07
REMARK 500 12 THR A 131 -63.99 67.88
REMARK 500
REMARK 500 THIS ENTRY HAS 94 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 TYR A 147 0.09 SIDE CHAIN
REMARK 500 1 ARG A 161 0.08 SIDE CHAIN
REMARK 500 1 ARG A 172 0.12 SIDE CHAIN
REMARK 500 1 TYR A 192 0.14 SIDE CHAIN
REMARK 500 2 TYR A 150 0.11 SIDE CHAIN
REMARK 500 2 TYR A 189 0.07 SIDE CHAIN
REMARK 500 2 TYR A 192 0.14 SIDE CHAIN
REMARK 500 3 TYR A 169 0.09 SIDE CHAIN
REMARK 500 3 ARG A 182 0.10 SIDE CHAIN
REMARK 500 4 TYR A 192 0.16 SIDE CHAIN
REMARK 500 5 ARG A 141 0.10 SIDE CHAIN
REMARK 500 5 TYR A 189 0.08 SIDE CHAIN
REMARK 500 5 TYR A 192 0.16 SIDE CHAIN
REMARK 500 6 TYR A 169 0.29 SIDE CHAIN
REMARK 500 6 TYR A 189 0.07 SIDE CHAIN
REMARK 500 8 TYR A 189 0.07 SIDE CHAIN
REMARK 500 8 TYR A 192 0.07 SIDE CHAIN
REMARK 500 9 PHE A 158 0.09 SIDE CHAIN
REMARK 500 9 TYR A 189 0.07 SIDE CHAIN
REMARK 500 9 TYR A 192 0.17 SIDE CHAIN
REMARK 500 9 ARG A 209 0.10 SIDE CHAIN
REMARK 500 10 TYR A 150 0.09 SIDE CHAIN
REMARK 500 10 PHE A 158 0.10 SIDE CHAIN
REMARK 500 10 ARG A 161 0.09 SIDE CHAIN
REMARK 500 10 TYR A 189 0.09 SIDE CHAIN
REMARK 500 10 TYR A 192 0.14 SIDE CHAIN
REMARK 500 11 PHE A 158 0.08 SIDE CHAIN
REMARK 500 11 TYR A 169 0.09 SIDE CHAIN
REMARK 500 11 ARG A 184 0.10 SIDE CHAIN
REMARK 500 11 TYR A 189 0.10 SIDE CHAIN
REMARK 500 11 TYR A 192 0.08 SIDE CHAIN
REMARK 500 12 TYR A 169 0.08 SIDE CHAIN
REMARK 500 13 TYR A 169 0.11 SIDE CHAIN
REMARK 500 13 ARG A 186 0.10 SIDE CHAIN
REMARK 500 13 TYR A 192 0.07 SIDE CHAIN
REMARK 500 14 TYR A 169 0.11 SIDE CHAIN
REMARK 500 14 ARG A 184 0.10 SIDE CHAIN
REMARK 500 14 TYR A 189 0.07 SIDE CHAIN
REMARK 500 14 TYR A 192 0.07 SIDE CHAIN
REMARK 500 15 TYR A 150 0.09 SIDE CHAIN
REMARK 500 15 TYR A 169 0.08 SIDE CHAIN
REMARK 500 16 ARG A 141 0.08 SIDE CHAIN
REMARK 500 16 TYR A 150 0.08 SIDE CHAIN
REMARK 500 16 TYR A 169 0.08 SIDE CHAIN
REMARK 500 16 TYR A 189 0.07 SIDE CHAIN
REMARK 500 17 ARG A 191 0.08 SIDE CHAIN
REMARK 500 17 TYR A 192 0.07 SIDE CHAIN
REMARK 500 18 TYR A 147 0.09 SIDE CHAIN
REMARK 500 18 TYR A 192 0.07 SIDE CHAIN
REMARK 500 19 TYR A 169 0.11 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 53 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 213 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 135 SG
REMARK 620 2 CYS A 138 SG 108.2
REMARK 620 3 CYS A 152 SG 110.0 108.5
REMARK 620 4 CYS A 155 SG 108.2 112.5 109.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 214 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 171 SG
REMARK 620 2 CYS A 177 SG 112.9
REMARK 620 3 CYS A 187 SG 107.7 110.8
REMARK 620 4 CYS A 190 SG 108.3 109.0 108.1
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 213
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 214
DBREF 1RXR A 130 212 UNP P19793 RXRA_HUMAN 130 212
SEQADV 1RXR ALA A 195 UNP P19793 CYS 195 ENGINEERED MUTATION
SEQRES 1 A 83 PHE THR LYS HIS ILE CYS ALA ILE CYS GLY ASP ARG SER
SEQRES 2 A 83 SER GLY LYS HIS TYR GLY VAL TYR SER CYS GLU GLY CYS
SEQRES 3 A 83 LYS GLY PHE PHE LYS ARG THR VAL ARG LYS ASP LEU THR
SEQRES 4 A 83 TYR THR CYS ARG ASP ASN LYS ASP CYS LEU ILE ASP LYS
SEQRES 5 A 83 ARG GLN ARG ASN ARG CYS GLN TYR CYS ARG TYR GLN LYS
SEQRES 6 A 83 ALA LEU ALA MET GLY MET LYS ARG GLU ALA VAL GLN GLU
SEQRES 7 A 83 GLU ARG GLN ARG GLY
HET ZN A 213 1
HET ZN A 214 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 GLU A 153 LYS A 165 1 13
HELIX 2 2 GLN A 188 MET A 198 1 11
HELIX 3 3 ARG A 202 GLU A 207 5 6
SHEET 1 A 2 GLY A 144 HIS A 146 0
SHEET 2 A 2 VAL A 149 SER A 151 -1 N SER A 151 O GLY A 144
LINK ZN ZN A 213 SG CYS A 135 1555 1555 2.29
LINK ZN ZN A 213 SG CYS A 138 1555 1555 2.30
LINK ZN ZN A 213 SG CYS A 152 1555 1555 2.30
LINK ZN ZN A 213 SG CYS A 155 1555 1555 2.30
LINK ZN ZN A 214 SG CYS A 171 1555 1555 2.30
LINK ZN ZN A 214 SG CYS A 177 1555 1555 2.30
LINK ZN ZN A 214 SG CYS A 187 1555 1555 2.30
LINK ZN ZN A 214 SG CYS A 190 1555 1555 2.30
SITE 1 AC1 4 CYS A 135 CYS A 138 CYS A 152 CYS A 155
SITE 1 AC2 4 CYS A 171 CYS A 177 CYS A 187 CYS A 190
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 - r 14 2 Bytes