Header list of 1d2j.pdb file
Complete list - 3 20 Bytes
HEADER SIGNALING PROTEIN 23-SEP-99 1D2J
TITLE LDL RECEPTOR LIGAND-BINDING MODULE 6
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN, SIXTH REPEAT;
COMPND 5 SYNONYM: LR6*;
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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMM-LR6*
KEYWDS RECEPTOR, LDLR, CYSTEINE-RICH MODULE, CALCIUM LIGAND-BINDING,
KEYWDS 2 FAMILIAL HYPERCHOLESTEROLEMIA, SIGNALING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR C.L.NORTH,S.C.BLACKLOW
REVDAT 3 03-NOV-21 1D2J 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 1D2J 1 VERSN
REVDAT 1 22-MAR-00 1D2J 0
JRNL AUTH C.L.NORTH,S.C.BLACKLOW
JRNL TITL SOLUTION STRUCTURE OF THE SIXTH LDL-A MODULE OF THE LDL
JRNL TITL 2 RECEPTOR.
JRNL REF BIOCHEMISTRY V. 39 2564 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 10704205
JRNL DOI 10.1021/BI992087A
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.L.NORTH,S.C.BLACKLOW
REMARK 1 TITL STRUCTURAL INDEPENDENCE OF LIGAND-BINDING MODULES FIVE AND
REMARK 1 TITL 2 SIX OF THE LDL RECEPTOR
REMARK 1 REF BIOCHEMISTRY V. 38 3926 1999
REMARK 1 REFN ISSN 0006-2960
REMARK 1 DOI 10.1021/BI9821622
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 97.0, X-PLOR 3.8.1
REMARK 3 AUTHORS : MSI (FELIX), A. BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 541 UNIQUE NOE DISTANCES, 3 DISULFIDE
REMARK 3 BONDS, 9 H-BONDS, 17 DISTANCES DEFINE THE CA++ BINDING SITE, 17
REMARK 3 PHI ANGLES DERIVED FROM J-HNHA MEASUREMENTS
REMARK 4
REMARK 4 1D2J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-99.
REMARK 100 THE DEPOSITION ID IS D_1000009734.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298
REMARK 210 PH : 5.2; 5.2; 5.2; 5.2
REMARK 210 IONIC STRENGTH : 10 MM; 10 MM; 10 MM; 10 MM
REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 1 MM LR6 U-15N; 10 MM CACL2; 1
REMARK 210 MM LR6 U-15N; 10 MM CACL2; 1 MM
REMARK 210 LR6 UNLABELED; 10 MM CACL2; 1 MM
REMARK 210 LR6 UNLABELED; 10 MM CACL2
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HYDROGEN
REMARK 210 EXCHANGE; 2D NOESY; HMQC-J
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 400 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5
REMARK 210 METHOD USED : SIMULATED ANNEALING IN TORSION
REMARK 210 ANGLE SPACE FOLLOWED BY
REMARK 210 SIMULATED ANNEALING REFINEMENT
REMARK 210 IN 3D COORDINATE SPACE.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 60
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: NULL
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: 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
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 ALA A 213 36.54 -153.02
REMARK 500 1 THR A 214 -0.76 73.08
REMARK 500 1 CYS A 215 -78.02 -116.02
REMARK 500 1 ASP A 218 60.15 173.96
REMARK 500 1 GLU A 219 -150.44 -117.72
REMARK 500 1 CYS A 234 76.99 37.69
REMARK 500 1 ASP A 235 29.11 -140.68
REMARK 500 1 GLU A 237 76.75 -152.69
REMARK 500 1 TYR A 238 90.90 -34.22
REMARK 500 1 LYS A 241 -42.27 70.43
REMARK 500 1 LEU A 243 99.81 72.94
REMARK 500 1 SER A 244 -27.08 -171.48
REMARK 500 1 GLU A 246 -43.53 -141.96
REMARK 500 1 VAL A 247 89.38 -33.41
REMARK 500 1 CYS A 249 -146.73 -124.61
REMARK 500 2 ALA A 213 28.79 -148.29
REMARK 500 2 CYS A 215 -71.84 -113.41
REMARK 500 2 ASP A 218 12.18 -144.88
REMARK 500 2 GLU A 219 -150.77 -89.78
REMARK 500 2 CYS A 234 91.83 34.18
REMARK 500 2 ASP A 235 21.22 -150.16
REMARK 500 2 TYR A 238 87.23 -67.00
REMARK 500 2 LYS A 241 -42.25 69.50
REMARK 500 2 LEU A 243 98.36 69.77
REMARK 500 2 SER A 244 -31.04 -164.45
REMARK 500 2 GLU A 246 -75.12 -127.38
REMARK 500 2 VAL A 247 77.27 0.69
REMARK 500 2 CYS A 249 -135.70 -88.25
REMARK 500 3 ALA A 213 39.62 -155.20
REMARK 500 3 THR A 214 -2.47 74.08
REMARK 500 3 CYS A 215 -80.02 -123.45
REMARK 500 3 ASP A 218 67.77 167.55
REMARK 500 3 GLU A 219 -149.64 -132.00
REMARK 500 3 CYS A 234 84.70 28.04
REMARK 500 3 ASP A 235 33.36 -143.43
REMARK 500 3 TYR A 238 75.47 -54.36
REMARK 500 3 LYS A 241 -43.55 70.50
REMARK 500 3 LEU A 243 98.04 67.80
REMARK 500 3 SER A 244 -32.44 -163.51
REMARK 500 3 GLU A 246 -74.46 -111.05
REMARK 500 3 VAL A 247 94.61 -44.87
REMARK 500 3 VAL A 250 28.07 37.15
REMARK 500 4 ALA A 213 53.61 -111.50
REMARK 500 4 THR A 214 -61.57 66.01
REMARK 500 4 GLU A 219 -151.65 -91.89
REMARK 500 4 CYS A 234 85.47 28.77
REMARK 500 4 ASP A 235 33.37 -145.18
REMARK 500 4 TYR A 238 75.52 -53.71
REMARK 500 4 LYS A 241 -42.88 70.82
REMARK 500 4 LEU A 243 95.93 67.94
REMARK 500
REMARK 500 THIS ENTRY HAS 273 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 ARG A 216 0.26 SIDE CHAIN
REMARK 500 1 ARG A 232 0.22 SIDE CHAIN
REMARK 500 1 ARG A 236 0.20 SIDE CHAIN
REMARK 500 2 ARG A 216 0.23 SIDE CHAIN
REMARK 500 2 ARG A 232 0.20 SIDE CHAIN
REMARK 500 2 ARG A 236 0.29 SIDE CHAIN
REMARK 500 3 ARG A 216 0.21 SIDE CHAIN
REMARK 500 3 ARG A 232 0.28 SIDE CHAIN
REMARK 500 3 ARG A 236 0.31 SIDE CHAIN
REMARK 500 4 ARG A 216 0.19 SIDE CHAIN
REMARK 500 4 ARG A 232 0.24 SIDE CHAIN
REMARK 500 4 ARG A 236 0.22 SIDE CHAIN
REMARK 500 5 ARG A 216 0.28 SIDE CHAIN
REMARK 500 5 ARG A 232 0.26 SIDE CHAIN
REMARK 500 5 ARG A 236 0.23 SIDE CHAIN
REMARK 500 6 ARG A 216 0.31 SIDE CHAIN
REMARK 500 6 ARG A 232 0.13 SIDE CHAIN
REMARK 500 6 ARG A 236 0.23 SIDE CHAIN
REMARK 500 7 ARG A 216 0.29 SIDE CHAIN
REMARK 500 7 ARG A 236 0.24 SIDE CHAIN
REMARK 500 8 ARG A 216 0.26 SIDE CHAIN
REMARK 500 8 ARG A 232 0.28 SIDE CHAIN
REMARK 500 8 ARG A 236 0.32 SIDE CHAIN
REMARK 500 9 ARG A 216 0.22 SIDE CHAIN
REMARK 500 9 ARG A 232 0.32 SIDE CHAIN
REMARK 500 9 ARG A 236 0.17 SIDE CHAIN
REMARK 500 10 ARG A 216 0.31 SIDE CHAIN
REMARK 500 10 ARG A 232 0.21 SIDE CHAIN
REMARK 500 10 ARG A 236 0.20 SIDE CHAIN
REMARK 500 11 ARG A 216 0.11 SIDE CHAIN
REMARK 500 11 ARG A 232 0.26 SIDE CHAIN
REMARK 500 11 ARG A 236 0.20 SIDE CHAIN
REMARK 500 12 ARG A 216 0.28 SIDE CHAIN
REMARK 500 12 ARG A 232 0.11 SIDE CHAIN
REMARK 500 12 ARG A 236 0.18 SIDE CHAIN
REMARK 500 13 ARG A 216 0.29 SIDE CHAIN
REMARK 500 13 ARG A 232 0.14 SIDE CHAIN
REMARK 500 13 ARG A 236 0.30 SIDE CHAIN
REMARK 500 14 ARG A 216 0.25 SIDE CHAIN
REMARK 500 14 ARG A 232 0.31 SIDE CHAIN
REMARK 500 14 ARG A 236 0.23 SIDE CHAIN
REMARK 500 15 ARG A 216 0.29 SIDE CHAIN
REMARK 500 15 ARG A 232 0.14 SIDE CHAIN
REMARK 500 15 ARG A 236 0.27 SIDE CHAIN
REMARK 500 16 ARG A 232 0.31 SIDE CHAIN
REMARK 500 16 ARG A 236 0.17 SIDE CHAIN
REMARK 500 17 ARG A 216 0.14 SIDE CHAIN
REMARK 500 17 ARG A 232 0.29 SIDE CHAIN
REMARK 500 17 ARG A 236 0.21 SIDE CHAIN
REMARK 500 18 ARG A 216 0.22 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 58 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 CA A 1 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ARG A 232 O
REMARK 620 2 ASP A 235 OD2 79.6
REMARK 620 3 GLU A 237 O 173.6 94.0
REMARK 620 4 ASP A 239 OD2 93.5 99.1 87.6
REMARK 620 5 ASP A 245 OD2 92.1 161.7 94.0 97.7
REMARK 620 6 GLU A 246 OE2 131.5 121.0 52.0 121.5 54.0
REMARK 620 7 GLU A 246 OE1 96.5 79.2 82.0 169.3 85.7 52.9
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AJJ RELATED DB: PDB
REMARK 900 MODULE PRECEEDING THIS ENTRY IN THE LDL RECEPTOR
DBREF 1D2J A 212 251 UNP P01130 LDLR_HUMAN 233 272
SEQADV 1D2J LEU A 243 UNP P01130 MET 264 ENGINEERED MUTATION
SEQRES 1 A 40 VAL ALA THR CYS ARG PRO ASP GLU PHE GLN CYS SER ASP
SEQRES 2 A 40 GLY ASN CYS ILE HIS GLY SER ARG GLN CYS ASP ARG GLU
SEQRES 3 A 40 TYR ASP CYS LYS ASP LEU SER ASP GLU VAL GLY CYS VAL
SEQRES 4 A 40 ASN
HET CA A 1 1
HETNAM CA CALCIUM ION
FORMUL 2 CA CA 2+
HELIX 1 1 HIS A 229 GLN A 233 5 5
SHEET 1 A 2 PHE A 220 CYS A 222 0
SHEET 2 A 2 ASN A 226 ILE A 228 -1 O ASN A 226 N CYS A 222
SSBOND 1 CYS A 215 CYS A 227 1555 1555 2.02
SSBOND 2 CYS A 222 CYS A 240 1555 1555 2.02
SSBOND 3 CYS A 234 CYS A 249 1555 1555 2.03
LINK CA CA A 1 O ARG A 232 1555 1555 2.55
LINK CA CA A 1 OD2 ASP A 235 1555 1555 2.53
LINK CA CA A 1 O GLU A 237 1555 1555 2.63
LINK CA CA A 1 OD2 ASP A 239 1555 1555 2.40
LINK CA CA A 1 OD2 ASP A 245 1555 1555 2.60
LINK CA CA A 1 OE2 GLU A 246 1555 1555 2.40
LINK CA CA A 1 OE1 GLU A 246 1555 1555 2.43
SITE 1 AC1 6 ARG A 232 ASP A 235 GLU A 237 ASP A 239
SITE 2 AC1 6 ASP A 245 GLU A 246
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 - 3 20 Bytes