HEADER HYDROLASE INHIBITOR 03-APR-06 2GKR TITLE CRYSTAL STRUCTURE OF THE N-TERMINALLY TRUNCATED OMTKY3- TITLE 2 DEL(1-5) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OVOMUCOID; COMPND 3 CHAIN: I; COMPND 4 FRAGMENT: TURKEY OVOMUCOID THIRD DOMAIN, DEL (1-5); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 3 ORGANISM_COMMON: TURKEY; SOURCE 4 ORGANISM_TAXID: 9103; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS REACTIVE-SITE LOOP, ALPHA-HELIX, ANTIPARALLEL BETA-SHEET, KEYWDS 2 HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR T.W.LEE,M.A.QASIM,M.LASKOWSKI JR.,M.N.G.JAMES REVDAT 3 24-FEB-09 2GKR 1 VERSN REVDAT 2 17-APR-07 2GKR 1 JRNL REVDAT 1 13-FEB-07 2GKR 0 JRNL AUTH T.W.LEE,M.A.QASIM,M.LASKOWSKI,M.N.JAMES JRNL TITL STRUCTURAL INSIGHTS INTO THE NON-ADDITIVITY JRNL TITL 2 EFFECTS IN THE SEQUENCE-TO-REACTIVITY ALGORITHM JRNL TITL 3 FOR SERINE PEPTIDASES AND THEIR INHIBITORS. JRNL REF J.MOL.BIOL. V. 367 527 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17266986 JRNL DOI 10.1016/J.JMB.2007.01.008 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 12224 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1348 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 824 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 392 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : -0.67000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.147 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 400 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 329 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 543 ; 1.672 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 782 ; 1.131 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 50 ; 6.224 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 17 ;27.370 ;25.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 65 ;10.225 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ;13.488 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 58 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 446 ; 0.025 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 75 ; 0.015 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 79 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 317 ; 0.156 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 209 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 224 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 31 ; 0.179 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.129 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 22 ; 0.285 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.233 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 333 ; 2.300 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 105 ; 1.209 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 409 ; 2.610 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 184 ; 2.718 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 134 ; 3.141 ; 3.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : I 6 I 56 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9880 -0.0590 3.2960 REMARK 3 T TENSOR REMARK 3 T11: -0.0394 T22: -0.0111 REMARK 3 T33: -0.0628 T12: 0.0045 REMARK 3 T13: -0.0014 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 3.1191 L22: 0.9447 REMARK 3 L33: 3.4575 L12: 0.5065 REMARK 3 L13: -0.8537 L23: -0.6098 REMARK 3 S TENSOR REMARK 3 S11: -0.0004 S12: -0.0098 S13: -0.0519 REMARK 3 S21: 0.0073 S22: 0.0084 S23: 0.0208 REMARK 3 S31: 0.0293 S32: -0.0426 S33: -0.0080 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2GKR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-06. REMARK 100 THE RCSB ID CODE IS RCSB037240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NA PH 7.5, 10% V/V REMARK 280 ISOPROPANOL, 20% W/V PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 17.21450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 300 REMARK: THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER WHICH REMARK 300 IS COMPLETELY INCLUDED IN EACH ASYMMETRIC UNIT. 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: I 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 ARG I 21 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES 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 ARG I 21 0.12 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL I 101 DBREF 2GKR I 6 56 UNP P68390 IOVO_MELGA 135 185 SEQRES 1 I 51 VAL ASP CYS SER GLU TYR PRO LYS PRO ALA CYS THR LEU SEQRES 2 I 51 GLU TYR ARG PRO LEU CYS GLY SER ASP ASN LYS THR TYR SEQRES 3 I 51 GLY ASN LYS CYS ASN PHE CYS ASN ALA VAL VAL GLU SER SEQRES 4 I 51 ASN GLY THR LEU THR LEU SER HIS PHE GLY LYS CYS HET CL I 101 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *63(H2 O) HELIX 1 1 ASN I 33 SER I 44 1 12 SHEET 1 A 3 THR I 30 TYR I 31 0 SHEET 2 A 3 LEU I 23 GLY I 25 -1 N LEU I 23 O TYR I 31 SHEET 3 A 3 LEU I 50 PHE I 53 -1 O HIS I 52 N CYS I 24 SSBOND 1 CYS I 8 CYS I 38 1555 1555 2.06 SSBOND 2 CYS I 16 CYS I 35 1555 1555 2.04 SSBOND 3 CYS I 24 CYS I 56 1555 1555 2.04 CISPEP 1 TYR I 11 PRO I 12 0 8.13 SITE 1 AC1 3 VAL I 6 LEU I 50 LYS I 55 CRYST1 22.900 34.429 25.794 90.00 97.25 90.00 P 1 21 1 2 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 0.043668 0.000000 0.005555 0.00000 SCALE2 0.000000 0.029045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039081 0.00000 MASTER 282 0 1 1 3 0 1 6 0 0 0 4 END