HEADER SIGNALING PROTEIN 27-OCT-00 1G4F TITLE NMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA2-GLYCOPROTEIN I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS SHORT CONSENSUS REPEAT, SUSHI-DOMAIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.HOSHINO,Y.HAGIHARA,I.NISHII,T.YAMAZAKI,H.KATO,Y.GOTO REVDAT 5 30-OCT-24 1G4F 1 REMARK REVDAT 4 23-FEB-22 1G4F 1 REMARK SEQADV REVDAT 3 24-FEB-09 1G4F 1 VERSN REVDAT 2 28-MAR-01 1G4F 1 JRNL REVDAT 1 15-NOV-00 1G4F 0 JRNL AUTH M.HOSHINO,Y.HAGIHARA,I.NISHII,T.YAMAZAKI,H.KATO,Y.GOTO JRNL TITL IDENTIFICATION OF THE PHOSPHOLIPID-BINDING SITE OF HUMAN JRNL TITL 2 BETA(2)-GLYCOPROTEIN I DOMAIN V BY HETERONUCLEAR MAGNETIC JRNL TITL 3 RESONANCE. JRNL REF J.MOL.BIOL. V. 304 927 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11124037 JRNL DOI 10.1006/JMBI.2000.4243 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.841, X-PLOR 3.841 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1402 RESTRAINTS, 1288 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 88 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 26 DISTANCE RESTRAINTS FROM HYDROGEN REMARK 3 BONDS REMARK 4 REMARK 4 1G4F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.12 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM BETA2-GLYCOPROTEIN I DOMAIN REMARK 210 V U-15N; 20MM NA-PHOSPHATE REMARK 210 BUFFER, PH 6.0; 90% H2O, 10% D2O; REMARK 210 1MM BETA2-GLYCOPROTEIN I DOMAIN REMARK 210 V U-15N,13C; 20MM NA-PHOSPHATE REMARK 210 BUFFER, PD 6.0; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_ROESY; HNCO-TROSY; REMARK 210 HMQC-J; HNHB; HN(CO)HB; N15-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 18 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 H CYS A 5 O MET A 31 1.48 REMARK 500 O ASP A 79 H ASP A 82 1.50 REMARK 500 H GLY A 34 O CYS A 56 1.50 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 LEU A 7 101.39 -40.84 REMARK 500 1 LYS A 11 41.32 -157.18 REMARK 500 1 PHE A 27 43.84 -109.62 REMARK 500 1 ASN A 29 40.13 -102.53 REMARK 500 1 ASP A 58 87.34 -50.51 REMARK 500 1 SER A 72 -91.25 47.29 REMARK 500 1 PHE A 75 -166.64 45.75 REMARK 500 1 TRP A 76 -167.23 63.33 REMARK 500 1 LYS A 77 32.69 -151.93 REMARK 500 1 THR A 78 80.53 -156.57 REMARK 500 1 SER A 81 -19.74 -49.28 REMARK 500 2 SER A 4 171.86 -49.49 REMARK 500 2 CYS A 5 -147.72 -100.77 REMARK 500 2 LEU A 7 99.32 -38.39 REMARK 500 2 LYS A 11 43.95 -160.36 REMARK 500 2 VAL A 14 -164.96 -117.56 REMARK 500 2 ASP A 53 145.17 -38.81 REMARK 500 2 ASP A 58 90.17 -33.58 REMARK 500 2 GLU A 62 78.72 -100.38 REMARK 500 2 VAL A 63 154.81 -43.62 REMARK 500 2 GLU A 69 86.08 -63.97 REMARK 500 2 PHE A 75 -154.28 -159.88 REMARK 500 2 LYS A 77 -36.61 -144.68 REMARK 500 2 THR A 78 87.66 47.00 REMARK 500 2 ASP A 79 -159.27 -87.62 REMARK 500 2 ALA A 80 -28.27 -39.43 REMARK 500 3 ALA A 3 -146.64 -86.34 REMARK 500 3 SER A 4 -157.78 -133.48 REMARK 500 3 LEU A 7 104.99 -45.41 REMARK 500 3 LYS A 11 40.20 -160.82 REMARK 500 3 ASN A 29 37.78 -99.86 REMARK 500 3 ASP A 58 73.56 -58.49 REMARK 500 3 HIS A 70 -68.62 -96.48 REMARK 500 3 SER A 71 -42.05 173.42 REMARK 500 3 SER A 72 99.70 63.69 REMARK 500 3 LEU A 73 -172.66 53.64 REMARK 500 3 TRP A 76 173.64 -59.82 REMARK 500 4 SER A 4 -155.95 -61.39 REMARK 500 4 CYS A 5 -163.25 -122.28 REMARK 500 4 LEU A 7 100.75 -41.14 REMARK 500 4 VAL A 9 -147.53 -106.23 REMARK 500 4 ASP A 58 98.61 -45.09 REMARK 500 4 PHE A 67 159.37 56.15 REMARK 500 4 LYS A 68 73.70 -110.30 REMARK 500 4 GLU A 69 -171.22 -64.38 REMARK 500 4 SER A 72 -141.97 -108.82 REMARK 500 4 LEU A 73 -160.33 46.26 REMARK 500 4 TRP A 76 55.63 -147.01 REMARK 500 4 THR A 78 72.34 52.45 REMARK 500 5 SER A 4 -172.69 -66.73 REMARK 500 REMARK 500 THIS ENTRY HAS 238 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 20 0.16 SIDE CHAIN REMARK 500 2 ARG A 20 0.18 SIDE CHAIN REMARK 500 3 ARG A 20 0.32 SIDE CHAIN REMARK 500 4 ARG A 20 0.29 SIDE CHAIN REMARK 500 5 ARG A 20 0.29 SIDE CHAIN REMARK 500 6 ARG A 20 0.21 SIDE CHAIN REMARK 500 7 ARG A 20 0.24 SIDE CHAIN REMARK 500 8 ARG A 20 0.28 SIDE CHAIN REMARK 500 9 ARG A 20 0.15 SIDE CHAIN REMARK 500 10 ARG A 20 0.24 SIDE CHAIN REMARK 500 11 ARG A 20 0.24 SIDE CHAIN REMARK 500 12 ARG A 20 0.28 SIDE CHAIN REMARK 500 13 ARG A 20 0.17 SIDE CHAIN REMARK 500 14 ARG A 20 0.20 SIDE CHAIN REMARK 500 15 ARG A 20 0.26 SIDE CHAIN REMARK 500 16 ARG A 20 0.26 SIDE CHAIN REMARK 500 17 ARG A 20 0.08 SIDE CHAIN REMARK 500 18 ARG A 20 0.29 SIDE CHAIN REMARK 500 19 ARG A 20 0.30 SIDE CHAIN REMARK 500 20 ARG A 20 0.27 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G4G RELATED DB: PDB REMARK 900 1G4G CONTAINS THE ENERGY MINIMIZED AVERAGE STRUCTURE OF THIS ENTRY DBREF 1G4F A 1 86 UNP P02749 APOH_HUMAN 260 345 SEQADV 1G4F THR A 1 UNP P02749 CYS 260 CONFLICT SEQADV 1G4F LEU A 7 UNP P02749 VAL 266 VARIANT SEQRES 1 A 86 THR LYS ALA SER CYS LYS LEU PRO VAL LYS LYS ALA THR SEQRES 2 A 86 VAL VAL TYR GLN GLY GLU ARG VAL LYS ILE GLN GLU LYS SEQRES 3 A 86 PHE LYS ASN GLY MET LEU HIS GLY ASP LYS VAL SER PHE SEQRES 4 A 86 PHE CYS LYS ASN LYS GLU LYS LYS CYS SER TYR THR GLU SEQRES 5 A 86 ASP ALA GLN CYS ILE ASP GLY THR ILE GLU VAL PRO LYS SEQRES 6 A 86 CYS PHE LYS GLU HIS SER SER LEU ALA PHE TRP LYS THR SEQRES 7 A 86 ASP ALA SER ASP VAL LYS PRO CYS HELIX 1 1 ILE A 23 PHE A 27 1 5 HELIX 2 2 ASP A 79 VAL A 83 5 5 SHEET 1 A 2 THR A 13 TYR A 16 0 SHEET 2 A 2 GLU A 19 LYS A 22 -1 O GLU A 19 N TYR A 16 SHEET 1 B 3 LYS A 36 ASN A 43 0 SHEET 2 B 3 CYS A 48 ILE A 57 -1 O CYS A 48 N ASN A 43 SHEET 3 B 3 THR A 60 ILE A 61 -1 O THR A 60 N ILE A 57 SSBOND 1 CYS A 5 CYS A 56 1555 1555 2.02 SSBOND 2 CYS A 41 CYS A 66 1555 1555 2.02 SSBOND 3 CYS A 48 CYS A 86 1555 1555 2.02 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