PDB Short entry for 2PJF HEADER HYDROLASE 16-APR-07 2PJF TITLE SOLUTION STRUCTURE OF RHODOSTOMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOSTOXIN-DISINTEGRIN RHODOSTOMIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-68; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CALLOSELASMA RHODOSTOMA; SOURCE 3 ORGANISM_COMMON: MALAYAN PIT VIPER; SOURCE 4 ORGANISM_TAXID: 8717; SOURCE 5 GENE: RHOD; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X33; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZAA KEYWDS DISINTEGRIN, RHODOSTOMIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.J.CHUANG,Y.C.CHEN,C.Y.CHEN,Y.T.CHANG REVDAT 4 16-MAR-22 2PJF 1 REMARK REVDAT 3 21-APR-09 2PJF 1 JRNL REMARK REVDAT 2 24-FEB-09 2PJF 1 VERSN REVDAT 1 08-MAY-07 2PJF 0 SPRSDE 08-MAY-07 2PJF 1JYP JRNL AUTH C.Y.CHEN,J.H.SHIU,Y.H.HSIEH,Y.C.LIU,Y.C.CHEN,Y.C.CHEN, JRNL AUTH 2 W.Y.JENG,M.J.TANG,S.J.LO,W.J.CHUANG JRNL TITL EFFECT OF D TO E MUTATION OF THE RGD MOTIF IN RHODOSTOMIN ON JRNL TITL 2 ITS ACTIVITY, STRUCTURE, AND DYNAMICS: IMPORTANCE OF THE JRNL TITL 3 INTERACTIONS BETWEEN THE D RESIDUE AND INTEGRIN JRNL REF PROTEINS 2009 JRNL REFN ESSN 1097-0134 JRNL PMID 19280603 JRNL DOI 10.1002/PROT.22387 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.185 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1014 RESTRAINTS, 944 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 55 DIHEDRAL ANGLE RESTRAINTS, 9 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS, 6 DISTANCE RESTRAINTS REMARK 3 FROM DISULFIDE BONDS REMARK 4 REMARK 4 2PJF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042442. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM RHODOSTOMIN, 90%H2O, 10%D2O; REMARK 210 2MM RHODOSTOMIN, 100%D2O; 2MM REMARK 210 RHODOSTOMIN U-15N, 90%H2O, 10% REMARK 210 D2O; 2MM RHODOSTOMIN U-15N, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_TOCSY; HNHA; 2D HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 3.1.7 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 ASP A 15 O LYS A 20 1.52 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 LYS A 2 48.96 -86.88 REMARK 500 1 ARG A 22 -64.57 -103.63 REMARK 500 1 SER A 39 -140.83 -67.76 REMARK 500 1 ILE A 44 107.85 -50.92 REMARK 500 1 ASP A 51 48.39 -140.80 REMARK 500 1 PRO A 65 -162.32 -77.95 REMARK 500 2 CYS A 32 53.47 -115.17 REMARK 500 2 SER A 39 -147.58 -64.92 REMARK 500 2 ILE A 44 101.42 -51.65 REMARK 500 3 PRO A 23 -162.24 -77.71 REMARK 500 3 SER A 39 -140.84 -64.34 REMARK 500 3 ILE A 44 74.63 -69.82 REMARK 500 3 ARG A 49 67.75 -101.74 REMARK 500 4 CYS A 19 38.98 33.63 REMARK 500 4 LEU A 21 107.14 -40.68 REMARK 500 4 PRO A 23 -167.71 -79.04 REMARK 500 4 PHE A 38 105.69 -55.08 REMARK 500 4 SER A 39 166.00 -44.71 REMARK 500 4 ALA A 41 167.98 -47.82 REMARK 500 4 ILE A 44 104.62 -49.31 REMARK 500 4 TYR A 67 50.15 -119.88 REMARK 500 5 LEU A 21 -173.27 -51.69 REMARK 500 5 ARG A 22 -65.73 -152.80 REMARK 500 5 CYS A 32 42.10 -95.33 REMARK 500 5 SER A 39 -146.05 -61.80 REMARK 500 5 ALA A 41 171.99 -48.65 REMARK 500 5 ILE A 44 94.54 -51.90 REMARK 500 6 ARG A 22 -61.10 -144.52 REMARK 500 6 SER A 39 -143.25 -63.74 REMARK 500 6 PRO A 65 -158.45 -79.25 REMARK 500 6 TYR A 67 55.22 -95.77 REMARK 500 7 ARG A 22 -62.10 -99.90 REMARK 500 7 PRO A 23 -159.47 -77.69 REMARK 500 7 GLU A 29 -165.12 -167.37 REMARK 500 7 CYS A 36 41.14 76.95 REMARK 500 7 SER A 39 -172.52 -62.44 REMARK 500 7 ALA A 41 163.69 -48.82 REMARK 500 7 ARG A 49 63.95 -100.42 REMARK 500 7 ASP A 51 51.13 -111.12 REMARK 500 8 LYS A 2 44.21 -148.60 REMARK 500 8 PRO A 23 -159.17 -78.83 REMARK 500 8 SER A 39 -168.02 -58.26 REMARK 500 8 ILE A 44 83.75 -54.71 REMARK 500 8 ASP A 51 37.78 -89.25 REMARK 500 8 PRO A 65 -156.35 -79.22 REMARK 500 8 TYR A 67 -39.35 -167.27 REMARK 500 9 GLU A 10 25.70 -147.92 REMARK 500 9 ARG A 22 -65.11 -100.39 REMARK 500 9 PRO A 23 -166.87 -76.01 REMARK 500 9 CYS A 36 41.17 72.51 REMARK 500 REMARK 500 THIS ENTRY HAS 129 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 22 0.20 SIDE CHAIN REMARK 500 1 ARG A 40 0.31 SIDE CHAIN REMARK 500 1 ARG A 46 0.32 SIDE CHAIN REMARK 500 1 ARG A 49 0.27 SIDE CHAIN REMARK 500 1 ARG A 56 0.31 SIDE CHAIN REMARK 500 1 ARG A 66 0.31 SIDE CHAIN REMARK 500 2 ARG A 22 0.25 SIDE CHAIN REMARK 500 2 ARG A 40 0.29 SIDE CHAIN REMARK 500 2 ARG A 46 0.27 SIDE CHAIN REMARK 500 2 ARG A 49 0.23 SIDE CHAIN REMARK 500 2 ARG A 56 0.22 SIDE CHAIN REMARK 500 2 ARG A 66 0.10 SIDE CHAIN REMARK 500 3 ARG A 22 0.18 SIDE CHAIN REMARK 500 3 ARG A 40 0.20 SIDE CHAIN REMARK 500 3 ARG A 49 0.14 SIDE CHAIN REMARK 500 3 ARG A 56 0.14 SIDE CHAIN REMARK 500 3 ARG A 66 0.24 SIDE CHAIN REMARK 500 4 ARG A 22 0.30 SIDE CHAIN REMARK 500 4 ARG A 40 0.16 SIDE CHAIN REMARK 500 4 ARG A 46 0.12 SIDE CHAIN REMARK 500 4 ARG A 49 0.23 SIDE CHAIN REMARK 500 4 ARG A 56 0.32 SIDE CHAIN REMARK 500 4 ARG A 66 0.27 SIDE CHAIN REMARK 500 5 ARG A 22 0.22 SIDE CHAIN REMARK 500 5 ARG A 40 0.31 SIDE CHAIN REMARK 500 5 ARG A 46 0.26 SIDE CHAIN REMARK 500 5 ARG A 49 0.30 SIDE CHAIN REMARK 500 5 ARG A 56 0.21 SIDE CHAIN REMARK 500 5 ARG A 66 0.25 SIDE CHAIN REMARK 500 6 ARG A 22 0.21 SIDE CHAIN REMARK 500 6 ARG A 40 0.26 SIDE CHAIN REMARK 500 6 ARG A 46 0.32 SIDE CHAIN REMARK 500 6 ARG A 49 0.23 SIDE CHAIN REMARK 500 6 ARG A 66 0.20 SIDE CHAIN REMARK 500 7 ARG A 22 0.09 SIDE CHAIN REMARK 500 7 ARG A 40 0.23 SIDE CHAIN REMARK 500 7 ARG A 46 0.09 SIDE CHAIN REMARK 500 7 ARG A 49 0.10 SIDE CHAIN REMARK 500 7 ARG A 56 0.32 SIDE CHAIN REMARK 500 7 ARG A 66 0.12 SIDE CHAIN REMARK 500 8 ARG A 22 0.25 SIDE CHAIN REMARK 500 8 ARG A 40 0.27 SIDE CHAIN REMARK 500 8 ARG A 46 0.32 SIDE CHAIN REMARK 500 8 ARG A 49 0.20 SIDE CHAIN REMARK 500 8 ARG A 56 0.32 SIDE CHAIN REMARK 500 8 ARG A 66 0.32 SIDE CHAIN REMARK 500 9 ARG A 22 0.30 SIDE CHAIN REMARK 500 9 ARG A 40 0.26 SIDE CHAIN REMARK 500 9 ARG A 46 0.30 SIDE CHAIN REMARK 500 9 ARG A 49 0.23 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 115 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5117 RELATED DB: BMRB DBREF 2PJF A 1 68 UNP P30403 DISR_AGKRH 408 475 SEQRES 1 A 68 GLY LYS GLU CYS ASP CYS SER SER PRO GLU ASN PRO CYS SEQRES 2 A 68 CYS ASP ALA ALA THR CYS LYS LEU ARG PRO GLY ALA GLN SEQRES 3 A 68 CYS GLY GLU GLY LEU CYS CYS GLU GLN CYS LYS PHE SER SEQRES 4 A 68 ARG ALA GLY LYS ILE CYS ARG ILE PRO ARG GLY ASP MET SEQRES 5 A 68 PRO ASP ASP ARG CYS THR GLY GLN SER ALA ASP CYS PRO SEQRES 6 A 68 ARG TYR HIS SHEET 1 A 2 CYS A 14 ASP A 15 0 SHEET 2 A 2 LYS A 20 LEU A 21 -1 O LYS A 20 N ASP A 15 SHEET 1 B 2 CYS A 33 GLU A 34 0 SHEET 2 B 2 LYS A 37 PHE A 38 -1 O LYS A 37 N GLU A 34 SHEET 1 C 2 ALA A 41 ARG A 46 0 SHEET 2 C 2 ASP A 55 THR A 58 -1 O CYS A 57 N GLY A 42 SSBOND 1 CYS A 4 CYS A 19 1555 1555 2.02 SSBOND 2 CYS A 6 CYS A 14 1555 1555 2.02 SSBOND 3 CYS A 13 CYS A 36 1555 1555 2.02 SSBOND 4 CYS A 27 CYS A 33 1555 1555 2.02 SSBOND 5 CYS A 32 CYS A 57 1555 1555 2.02 SSBOND 6 CYS A 45 CYS A 64 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