HEADER CELL ADHESION 24-MAR-04 1SSU TITLE STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR DISULFIDE BOND HETEROGENEITY TITLE 2 IN ACTIVE FORMS OF THE SOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITRONECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VTN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21TRXB(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-32A KEYWDS SOMATOSTATIN B DOMAIN, VITRONECTIN, DISULFIDE BONDS HETEROGENEITY, KEYWDS 2 CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.KAMIKUBO,R.DE GUZMAN,G.KROON,S.CURRIDEN,J.G.NEELS,M.J.CHURCHILL, AUTHOR 2 P.DAWSON,S.OLDZIEJ,A.JAGIELSKA,H.A.SCHERAGA,D.J.LOSKUTOFF,H.J.DYSON REVDAT 4 20-NOV-24 1SSU 1 REMARK REVDAT 3 02-MAR-22 1SSU 1 REMARK REVDAT 2 24-FEB-09 1SSU 1 VERSN REVDAT 1 27-JUL-04 1SSU 0 JRNL AUTH Y.KAMIKUBO,R.DE GUZMAN,G.KROON,S.CURRIDEN,J.G.NEELS, JRNL AUTH 2 M.J.CHURCHILL,P.DAWSON,S.OLDZIEJ,A.JAGIELSKA,H.A.SCHERAGA, JRNL AUTH 3 D.J.LOSKUTOFF,H.J.DYSON JRNL TITL DISULFIDE BONDING ARRANGEMENTS IN ACTIVE FORMS OF THE JRNL TITL 2 SOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN. JRNL REF BIOCHEMISTRY V. 43 6519 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15157085 JRNL DOI 10.1021/BI049647C REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, AMBER 7 REMARK 3 AUTHORS : PETER GUNTERT (DYANA), D. CASE, D. PEARLMAN ET AL. REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SSU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021972. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 180 MM; 180 MM REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : N15-LABELED PROTEIN 20 MM SODIUM REMARK 210 PHOSPHATE PH 7.5; UNLABELED REMARK 210 PROTEIN 20 MM SODIUM PHOSPHATE REMARK 210 PH 7.5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 7, NMRPIPE 2003, NMRVIEW REMARK 210 4.1.3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS IN DYANA REMARK 210 FOLLOWED BY SIMULATED ANNEALING REMARK 210 AND ENERGY MINIMIZATION IN AMBER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 LOWEST ENERGY STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NOT APPLICABLE 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 1 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 10 CYS A 21 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 10 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 12 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 16 CYS A 5 CA - CB - SG ANGL. DEV. = 9.0 DEGREES REMARK 500 17 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 CYS A 5 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 18 CYS A 21 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 20 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 20 CYS A 39 CA - CB - SG ANGL. DEV. = 8.1 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 ASN A 14 89.41 -160.53 REMARK 500 1 CYS A 21 48.15 -75.84 REMARK 500 1 ASP A 34 38.65 -143.43 REMARK 500 1 PRO A 41 158.83 -46.13 REMARK 500 1 PHE A 49 30.82 -146.26 REMARK 500 2 ASN A 14 98.17 -167.87 REMARK 500 2 CYS A 32 155.71 -48.33 REMARK 500 2 LYS A 40 109.21 -40.25 REMARK 500 2 PHE A 49 -43.75 -164.87 REMARK 500 2 THR A 50 21.10 -140.23 REMARK 500 3 LYS A 6 90.57 -69.71 REMARK 500 3 ARG A 8 -30.53 -134.11 REMARK 500 3 ASN A 14 84.65 -161.01 REMARK 500 3 CYS A 21 46.88 -74.43 REMARK 500 3 ASP A 34 38.45 -141.44 REMARK 500 4 ASN A 14 114.08 -163.42 REMARK 500 4 GLN A 20 64.84 -109.20 REMARK 500 4 CYS A 21 42.36 -69.30 REMARK 500 5 LYS A 6 91.07 -69.74 REMARK 500 5 ARG A 8 -35.04 -132.10 REMARK 500 5 ASN A 14 89.87 -164.70 REMARK 500 5 VAL A 15 -8.21 -58.89 REMARK 500 5 GLN A 20 66.88 -102.45 REMARK 500 5 CYS A 21 47.90 -72.67 REMARK 500 5 ASP A 34 32.56 -140.50 REMARK 500 5 TYR A 35 -56.11 -29.82 REMARK 500 5 LYS A 40 105.38 -38.51 REMARK 500 5 PRO A 41 -169.46 -79.05 REMARK 500 5 GLN A 42 150.90 -49.90 REMARK 500 6 CYS A 9 124.61 -38.16 REMARK 500 6 GLN A 20 65.01 -100.31 REMARK 500 6 CYS A 21 38.43 -67.15 REMARK 500 6 ASP A 47 28.70 -141.92 REMARK 500 7 CYS A 21 38.48 -73.32 REMARK 500 7 LYS A 40 101.51 -37.27 REMARK 500 7 PRO A 41 16.31 -62.50 REMARK 500 8 LYS A 6 79.96 -69.47 REMARK 500 8 ASN A 14 103.16 -160.73 REMARK 500 8 CYS A 21 33.48 -65.91 REMARK 500 8 ASP A 34 40.77 -144.13 REMARK 500 8 PRO A 41 -176.62 -57.14 REMARK 500 9 LYS A 6 97.33 -69.69 REMARK 500 9 CYS A 9 15.48 -53.91 REMARK 500 9 THR A 10 15.60 -142.28 REMARK 500 9 GLN A 20 65.02 -111.36 REMARK 500 9 VAL A 43 39.38 -74.14 REMARK 500 10 LYS A 6 89.13 -69.86 REMARK 500 10 CYS A 21 36.66 -72.11 REMARK 500 10 CYS A 32 147.26 -39.83 REMARK 500 10 LYS A 40 106.87 -40.93 REMARK 500 REMARK 500 THIS ENTRY HAS 120 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 11 TYR A 35 0.07 SIDE CHAIN REMARK 500 16 TYR A 35 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1SSU A 1 51 UNP P04004 VTNC_HUMAN 20 70 SEQRES 1 A 51 ASP GLN GLU SER CYS LYS GLY ARG CYS THR GLU GLY PHE SEQRES 2 A 51 ASN VAL ASP LYS LYS CYS GLN CYS ASP GLU LEU CYS SER SEQRES 3 A 51 TYR TYR GLN SER CYS CYS THR ASP TYR THR ALA GLU CYS SEQRES 4 A 51 LYS PRO GLN VAL THR ARG GLY ASP VAL PHE THR MET HELIX 1 1 LEU A 24 TYR A 28 5 5 HELIX 2 2 ASP A 34 CYS A 39 1 6 SSBOND 1 CYS A 5 CYS A 9 1555 1555 2.04 SSBOND 2 CYS A 19 CYS A 21 1555 1555 2.06 SSBOND 3 CYS A 25 CYS A 31 1555 1555 2.02 SSBOND 4 CYS A 32 CYS A 39 1555 1555 2.04 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