10 20 30 40 50 60 70 80 1BR9 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEINASE INHIBITOR 28-AUG-98 1BR9
TITLE HUMAN TISSUE INHIBITOR OF METALLOPROTEINASE-2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLOPROTEINASE-2 INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TIMP-2, TISSUE INHIBITOR OF METALLOPROTEINASE-2; 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 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: H5; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS
KEYWDS PROTEINASE INHIBITOR
EXPDTA X-RAY DIFFRACTION
AUTHOR A.TUUTTILA,E.MORGUNOVA,U.BERGMANN,Y.LINDQVIST,K.TRYGGVASON, AUTHOR 2 G.SCHNEIDER
REVDAT 2 24-FEB-09 1BR9 1 VERSN REVDAT 1 04-MAY-99 1BR9 0
JRNL AUTH A.TUUTTILA,E.MORGUNOVA,U.BERGMANN,Y.LINDQVIST, JRNL AUTH 2 K.MASKOS,C.FERNANDEZ-CATALAN,W.BODE,K.TRYGGVASON, JRNL AUTH 3 G.SCHNEIDER JRNL TITL THREE-DIMENSIONAL STRUCTURE OF HUMAN TISSUE JRNL TITL 2 INHIBITOR OF METALLOPROTEINASES-2 AT 2.1 A JRNL TITL 3 RESOLUTION. JRNL REF J.MOL.BIOL. V. 284 1133 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9837731 JRNL DOI 10.1006/JMBI.1998.2223
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 10532 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 528 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1419 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 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) : 34.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.007 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.024 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL REFINEMENT WITH X-PLOR, THEN REMARK 3 REFMAC
REMARK 4 REMARK 4 1BR9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9095 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10532 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 10.000 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28400 REMARK 200 R SYM FOR SHELL (I) : 0.28400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: BOVINE TISSUE INHIBITOR, FERNANDEZ-CATALAN ET REMARK 200 AL., 1998, EMBO J., IN PRESS REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 36.02500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.02500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.35000 REMARK 290 SMTRY3 4 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 183 REMARK 465 PRO A 184 REMARK 465 LYS A 185 REMARK 465 GLN A 186 REMARK 465 GLU A 187 REMARK 465 PHE A 188 REMARK 465 LEU A 189 REMARK 465 ASP A 190 REMARK 465 ILE A 191 REMARK 465 GLU A 192 REMARK 465 ASP A 193 REMARK 465 PRO A 194
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 MET A 96 CA - CB - CG ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 132 CD - NE - CZ ANGL. DEV. = 8.5 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 ASP A 34 -169.56 -75.20 REMARK 500 LYS A 81 -96.55 -88.73 REMARK 500 HIS A 120 -28.42 -171.30 REMARK 500 ASP A 144 30.53 -87.83 REMARK 500 LYS A 155 2.15 82.34 REMARK 500 ASN A 158 45.15 -109.15 REMARK 500 ASP A 172 -8.26 158.39 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 256 DISTANCE = 9.68 ANGSTROMS
DBREF 1BR9 A 1 194 UNP P16035 TIMP2_HUMAN 27 220
SEQRES 1 A 194 CYS SER CYS SER PRO VAL HIS PRO GLN GLN ALA PHE CYS SEQRES 2 A 194 ASN ALA ASP VAL VAL ILE ARG ALA LYS ALA VAL SER GLU SEQRES 3 A 194 LYS GLU VAL ASP SER GLY ASN ASP ILE TYR GLY ASN PRO SEQRES 4 A 194 ILE LYS ARG ILE GLN TYR GLU ILE LYS GLN ILE LYS MET SEQRES 5 A 194 PHE LYS GLY PRO GLU LYS ASP ILE GLU PHE ILE TYR THR SEQRES 6 A 194 ALA PRO SER SER ALA VAL CYS GLY VAL SER LEU ASP VAL SEQRES 7 A 194 GLY GLY LYS LYS GLU TYR LEU ILE ALA GLY LYS ALA GLU SEQRES 8 A 194 GLY ASP GLY LYS MET HIS ILE THR LEU CYS ASP PHE ILE SEQRES 9 A 194 VAL PRO TRP ASP THR LEU SER THR THR GLN LYS LYS SER SEQRES 10 A 194 LEU ASN HIS ARG TYR GLN MET GLY CYS GLU CYS LYS ILE SEQRES 11 A 194 THR ARG CYS PRO MET ILE PRO CYS TYR ILE SER SER PRO SEQRES 12 A 194 ASP GLU CYS LEU TRP MET ASP TRP VAL THR GLU LYS ASN SEQRES 13 A 194 ILE ASN GLY HIS GLN ALA LYS PHE PHE ALA CYS ILE LYS SEQRES 14 A 194 ARG SER ASP GLY SER CYS ALA TRP TYR ARG GLY ALA ALA SEQRES 15 A 194 PRO PRO LYS GLN GLU PHE LEU ASP ILE GLU ASP PRO
FORMUL 2 HOH *63(H2 O)
HELIX 1 1 PRO A 8 ASN A 14 1 7 HELIX 2 2 SER A 69 VAL A 71 5 3 HELIX 3 3 TRP A 107 THR A 109 5 3 HELIX 4 4 THR A 112 ASN A 119 1 8 HELIX 5 5 GLN A 123 GLY A 125 5 3 HELIX 6 6 ASP A 150 GLU A 154 1 5 HELIX 7 7 HIS A 160 PHE A 164 1 5
SHEET 1 A 4 ILE A 104 PRO A 106 0 SHEET 2 A 4 GLU A 83 GLY A 88 -1 N LEU A 85 O VAL A 105 SHEET 3 A 4 VAL A 17 LYS A 22 -1 N ALA A 21 O TYR A 84 SHEET 4 A 4 LYS A 51 LYS A 54 -1 N LYS A 54 O VAL A 18 SHEET 1 B 5 LYS A 89 GLY A 92 0 SHEET 2 B 5 LYS A 95 ILE A 98 -1 N HIS A 97 O LYS A 89 SHEET 3 B 5 PHE A 62 THR A 65 1 N PHE A 62 O MET A 96 SHEET 4 B 5 LYS A 41 GLN A 49 -1 N TYR A 45 O ILE A 63 SHEET 5 B 5 ALA A 21 ASP A 30 -1 N VAL A 29 O ARG A 42 SHEET 1 C 2 LYS A 129 ARG A 132 0 SHEET 2 C 2 GLU A 145 TRP A 148 1 N CYS A 146 O LYS A 129 SHEET 1 D 2 ALA A 166 LYS A 169 0 SHEET 2 D 2 CYS A 175 TYR A 178 -1 N TYR A 178 O ALA A 166
SSBOND 1 CYS A 1 CYS A 72 1555 1555 2.01 SSBOND 2 CYS A 3 CYS A 101 1555 1555 2.03 SSBOND 3 CYS A 13 CYS A 126 1555 1555 2.05 SSBOND 4 CYS A 128 CYS A 175 1555 1555 2.03 SSBOND 5 CYS A 133 CYS A 138 1555 1555 2.03 SSBOND 6 CYS A 146 CYS A 167 1555 1555 2.00
CISPEP 1 ILE A 136 PRO A 137 0 5.83
CRYST1 72.050 52.700 46.100 90.00 90.00 90.00 P 21 21 2 4
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 0.013879 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018975 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021692 0.00000