PDB Short entry for 1EQK HEADER HYDROLASE INHIBITOR 05-APR-00 1EQK TITLE SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHIBITOR TITLE 2 OF THE RICE, ORYZA SATIVA L. JAPONICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORYZACYSTATIN-I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP; SOURCE 3 ORGANISM_TAXID: 39947; SOURCE 4 STRAIN: JAPONICA GROUP; SOURCE 5 TISSUE: SEED; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PLASMID PET-26B(+) KEYWDS ALPHA AND BETA PROTEINS, CYSTATIN-LIKE FOLD, CYSTATIN/MONELLIN KEYWDS 2 SUPERFAMILY, PHYTOCYSTATIN FAMILY, HYDROLASE INHIBITOR EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR K.NAGATA,N.KUDO,K.ABE,S.ARAI,M.TANOKURA REVDAT 3 16-FEB-22 1EQK 1 REMARK REVDAT 2 24-FEB-09 1EQK 1 VERSN REVDAT 1 10-JAN-01 1EQK 0 JRNL AUTH K.NAGATA,N.KUDO,K.ABE,S.ARAI,M.TANOKURA JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A JRNL TITL 2 CYSTEINE PROTEINASE INHIBITOR OF THE RICE, ORYZA SATIVA L. JRNL TITL 3 JAPONICA. JRNL REF BIOCHEMISTRY V. 39 14753 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11101290 JRNL DOI 10.1021/BI0006971 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.3B, CNS 0.9 REMARK 3 AUTHORS : VARIAN (VNMR), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES,PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 1383 RESTRAINTS, CONSISTING REMARK 3 OF 1183 INTERPROTON DISTANCE RESTRAINTS (338 LONG-RANGE (|I - J| REMARK 3 >= 6), 228 MEDIUM-RANGE (2 <= |I - J| <= 5), 351 SEQUENTIAL (|I - REMARK 3 J| = 1) AND 266 INTRARESIDUAL (|I - J| = 0)), 108 HYDROGEN BOND REMARK 3 RESTRAINTS (REPRESENTING 54 HYDROGEN BONDS) AND 92 TORSION ANGLE REMARK 3 RESTRAINTS (54 PHI AND 38 CHI1), WERE USED IN THE STRUCTURE REMARK 3 CALCULATIONS BY TORSION ANGLE DYNAMICS USING DYANA (VER. 1.4). A REMARK 3 FINAL SET OF 20 STRUCTURES WAS SELECTED FROM 100 CALCULATIONS ON REMARK 3 THE BASIS OF AGREEMENT WITH THE EXPERIMENTAL DATA AND VAN DER REMARK 3 WAALS' ENERGY. THE AVERAGE COORDINATES OF THE 20 DYANA REMARK 3 STRUCTURES WERE SUBJECTED TO ENERGY-MINIMIZATION USING CNS (VER. REMARK 3 0.9). REMARK 4 REMARK 4 1EQK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010822. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3 MM ORYZACYSTATIN-I; 50 MM REMARK 210 SODIUM PHOSPHATE/100 MM NACL/ REMARK 210 0.02% NAN3, PH 6.8; 10% D2O/90% REMARK 210 H2O; 2 MM ORYZACYSTATIN-I U-15N; REMARK 210 50 MM SODIUM PHOSPHATE/100 MM REMARK 210 NACL/0.02% NAN3, PH 6.8; 10% D2O/ REMARK 210 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.6, NMRDRAW 1.6, FELIX REMARK 210 95, PIPP/CAPP 4.0, DYANA 1.4, REMARK 210 AQUA 2.0, PROCHECK-NMR 3.4, REMARK 210 MOLMOL 2.6 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 21 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 1H AND 15N NMR REMARK 210 SPECTROSCOPY. 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 SER A 2 107.02 179.46 REMARK 500 1 SER A 3 131.76 -175.26 REMARK 500 1 ASP A 4 112.93 -174.87 REMARK 500 1 LEU A 9 3.89 -155.99 REMARK 500 1 VAL A 12 75.77 38.00 REMARK 500 1 ASN A 17 84.12 51.51 REMARK 500 1 GLU A 18 -17.88 -46.19 REMARK 500 1 THR A 32 -70.22 -61.29 REMARK 500 1 SER A 40 154.87 75.73 REMARK 500 1 LEU A 41 -43.15 -159.31 REMARK 500 1 LYS A 46 -170.21 -179.20 REMARK 500 1 VAL A 55 -118.34 -156.11 REMARK 500 1 TRP A 84 -19.14 -46.68 REMARK 500 1 MET A 85 14.71 -142.45 REMARK 500 1 ASP A 86 81.57 37.35 REMARK 500 1 GLU A 92 136.01 164.84 REMARK 500 1 VAL A 96 83.88 50.18 REMARK 500 1 ASN A 101 130.09 179.17 REMARK 500 2 VAL A 15 -165.38 -126.33 REMARK 500 2 ASN A 17 101.61 173.48 REMARK 500 2 THR A 32 -70.23 -70.83 REMARK 500 2 ASN A 39 25.78 43.35 REMARK 500 2 SER A 40 153.37 74.22 REMARK 500 2 LEU A 41 -15.21 -160.08 REMARK 500 2 LYS A 46 -175.98 -177.22 REMARK 500 2 VAL A 55 -118.98 -155.63 REMARK 500 2 TRP A 84 -14.98 -46.45 REMARK 500 2 MET A 85 10.35 -146.93 REMARK 500 2 ASP A 86 83.03 42.53 REMARK 500 2 LYS A 88 149.27 -178.44 REMARK 500 2 GLU A 89 115.09 -161.78 REMARK 500 2 GLU A 92 135.51 164.31 REMARK 500 2 VAL A 96 88.92 55.50 REMARK 500 2 ALA A 98 -29.74 -171.73 REMARK 500 2 SER A 99 -172.44 62.52 REMARK 500 2 ALA A 100 -80.16 75.47 REMARK 500 2 ASN A 101 -54.85 -149.11 REMARK 500 3 SER A 2 25.76 -143.07 REMARK 500 3 ASN A 17 82.96 60.00 REMARK 500 3 THR A 32 -72.08 -70.92 REMARK 500 3 SER A 40 150.63 75.31 REMARK 500 3 LEU A 41 -39.85 -151.36 REMARK 500 3 LEU A 42 -155.34 -162.78 REMARK 500 3 LYS A 46 -168.13 -178.47 REMARK 500 3 SER A 49 -169.13 -161.31 REMARK 500 3 VAL A 55 -119.45 -154.58 REMARK 500 3 TRP A 84 -15.14 -46.72 REMARK 500 3 ASP A 86 82.64 43.63 REMARK 500 3 GLU A 92 164.98 170.06 REMARK 500 3 PHE A 93 96.90 -161.98 REMARK 500 REMARK 500 THIS ENTRY HAS 379 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1EQK A 1 102 UNP P09229 CYT1_ORYSA 1 102 SEQRES 1 A 102 MET SER SER ASP GLY GLY PRO VAL LEU GLY GLY VAL GLU SEQRES 2 A 102 PRO VAL GLY ASN GLU ASN ASP LEU HIS LEU VAL ASP LEU SEQRES 3 A 102 ALA ARG PHE ALA VAL THR GLU HIS ASN LYS LYS ALA ASN SEQRES 4 A 102 SER LEU LEU GLU PHE GLU LYS LEU VAL SER VAL LYS GLN SEQRES 5 A 102 GLN VAL VAL ALA GLY THR LEU TYR TYR PHE THR ILE GLU SEQRES 6 A 102 VAL LYS GLU GLY ASP ALA LYS LYS LEU TYR GLU ALA LYS SEQRES 7 A 102 VAL TRP GLU LYS PRO TRP MET ASP PHE LYS GLU LEU GLN SEQRES 8 A 102 GLU PHE LYS PRO VAL ASP ALA SER ALA ASN ALA HELIX 1 1 ASP A 20 ALA A 38 1 19 SHEET 1 A 5 GLU A 13 VAL A 15 0 SHEET 2 A 5 LEU A 42 VAL A 54 -1 N VAL A 50 O VAL A 15 SHEET 3 A 5 THR A 58 GLU A 68 -1 O LEU A 59 N GLN A 53 SHEET 4 A 5 LYS A 73 GLU A 81 -1 N LYS A 73 O VAL A 66 SHEET 5 A 5 LEU A 90 LYS A 94 -1 N GLN A 91 O LYS A 78 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