PDB Short entry for 1D2B HEADER HYDROLASE INHIBITOR 22-SEP-99 1D2B TITLE THE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR OF TITLE 2 METALLOPROTEINASES-1 (N-TIMP-1), SOLUTION NMR, 29 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLOPROTEINASE INHIBITOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NTR DOMAIN, RESIDUES 24-149; COMPND 5 SYNONYM: TISSUE INHIBITOR OF METALLOPROTEINASES-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELLULAR_LOCATION: EXTRACELLULAR MATRIX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 10 OTHER_DETAILS: THIS IS THE FIRST 126 RESIDUES OF THE FULL LENGTH OF SOURCE 11 184 RESIDUES NATURALLY OCCURRING IN HUMANS. THE 126 RESIDUE SOURCE 12 RECOMBINANT N-TERMINAL DOMAIN LACKS THE NATURAL N-LINKED SOURCE 13 GLYCOSYLATION OF ASN30 AND ASN78. KEYWDS OB-FOLD, BETA BARREL, PROTEASE INHIBITOR, MMP INHIBITOR, HYDROLASE KEYWDS 2 INHIBITOR EXPDTA SOLUTION NMR NUMMDL 29 AUTHOR B.WU,S.ARUMUGAM,V.SEMENCHENKO,K.BREW,S.R.VAN DOREN REVDAT 4 23-MAR-22 1D2B 1 COMPND SOURCE JRNL REMARK REVDAT 3 24-FEB-09 1D2B 1 VERSN REVDAT 2 01-APR-03 1D2B 1 JRNL REVDAT 1 22-DEC-99 1D2B 0 JRNL AUTH B.WU,S.ARUMUGAM,G.GAO,G.I.LEE,V.SEMENCHENKO,W.HUANG,K.BREW, JRNL AUTH 2 S.R.VAN DOREN JRNL TITL NMR STRUCTURE OF TISSUE INHIBITOR OF METALLOPROTEINASES-1 JRNL TITL 2 IMPLICATES LOCALIZED INDUCED FIT IN RECOGNITION OF MATRIX JRNL TITL 3 METALLOPROTEINASES. JRNL REF J.MOL.BIOL. V. 295 257 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10623524 JRNL DOI 10.1006/JMBI.1999.3362 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.WU,S.ARUMUGAM,W.HUANG,K.BREW,S.R.VAN DOREN REMARK 1 TITL 1H, 13C AND 15N RESONANCE ASSIGNMENTS AND SECONDARY REMARK 1 TITL 2 STRUCTURE OF THE N- TERMINAL DOMAIN OF HUMAN TISSUE REMARK 1 TITL 3 INHIBITOR OF METALLOPROTEINASES-1 REMARK 1 REF J.BIOMOL.NMR V. 14 289 1999 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 10481281 REMARK 1 DOI 10.1023/A:1008310807946 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.6 REMARK 3 AUTHORS : BRUNGER,A.T., ADAMS,P.D., CLORE,G.M., WARREN,G.L. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MODEL 22 IS CLOSEST TO THE AVERAGE REMARK 3 WHILE MODEL 3 REPRESENTS THE CONFORMER WITH THE FEWEST VIOLATIONS REMARK 4 REMARK 4 1D2B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009726. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.171 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM N-TIMP-1 U-15N; 0.9 MM N REMARK 210 -TIMP-1 U-15N,13C; 0.7 MM N-TIMP- REMARK 210 1 U-15N,13C; 0.4 MM N-TIMP-1 16% REMARK 210 13C; 0.4 MM N-TIMP-1 U-15N,13C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D TIME REMARK 210 -SHARED NOESY-(13C,15N)-HSQC; 3D REMARK 210 13C FSCT-HSMQC-NOESY; 3D 13C REMARK 210 NOESY-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SYBYL TRIAD V6.2 OR V.6.3, CNS REMARK 210 0.6 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS FOLLOWED REMARK 210 BY CARTESIAN SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 120 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 29 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 3D HNHB, 3D HACAHB-COSY, 2D HMQC-J, 3D COUPLED HCACO, 3D REMARK 210 HNCA-J, {15N} SPIN- ECHO DIFFERENCE 13C CT-HSQC, {13CO} SPIN- REMARK 210 ECHO DIFFERENCE 13C CT-HSQC, 2D HN(CG) , 2D HN(COCG), 15N IPAP- REMARK 210 HSQC, 3D 13CA-COUPLED HNCO, 13C'-COUPLED IN-PHASE 15N HSQC 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 HG1 THR A 63 HA2 GLY A 71 0.72 REMARK 500 HB2 GLN A 9 HA GLU A 125 1.10 REMARK 500 HA2 GLY A 115 HG1 THR A 119 1.16 REMARK 500 O LEU A 34 H ALA A 65 1.22 REMARK 500 HG2 PRO A 8 HB3 GLU A 126 1.32 REMARK 500 HB VAL A 61 HD12 ILE A 96 1.32 REMARK 500 HA2 GLY A 115 OG1 THR A 119 1.49 REMARK 500 O PRO A 8 H PHE A 12 1.50 REMARK 500 H GLN A 36 O THR A 63 1.54 REMARK 500 O TRP A 105 H LEU A 108 1.54 REMARK 500 O ARG A 20 HG1 THR A 43 1.55 REMARK 500 H GLN A 90 O LEU A 93 1.55 REMARK 500 OG1 THR A 33 H TYR A 35 1.57 REMARK 500 O LEU A 17 H GLY A 87 1.57 REMARK 500 H VAL A 18 O LYS A 47 1.58 REMARK 500 HD2 TYR A 46 O PHE A 116 1.60 REMARK 500 HG1 THR A 63 CA GLY A 71 1.60 REMARK 500 O LEU A 34 N ALA A 65 2.01 REMARK 500 REMARK 500 REMARK: NULL 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 17 TYR A 35 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 17 TYR A 35 CB - CG - CD1 ANGL. DEV. = 3.7 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 THR A 2 84.03 -59.04 REMARK 500 1 HIS A 7 125.39 -28.46 REMARK 500 1 THR A 33 -53.04 -124.30 REMARK 500 1 LEU A 34 -7.77 90.58 REMARK 500 1 LEU A 52 67.57 -69.53 REMARK 500 1 ASP A 54 -85.13 -96.92 REMARK 500 1 ALA A 55 -40.28 -149.93 REMARK 500 1 ALA A 65 39.55 -95.80 REMARK 500 1 CYS A 70 58.65 -113.07 REMARK 500 1 TYR A 72 82.81 -167.19 REMARK 500 1 PHE A 73 97.36 -68.97 REMARK 500 1 ARG A 75 73.15 -117.26 REMARK 500 1 ASP A 91 28.83 41.75 REMARK 500 1 THR A 98 5.27 -69.20 REMARK 500 1 ASN A 106 -17.98 -45.12 REMARK 500 1 LYS A 118 -37.68 -141.07 REMARK 500 1 CYS A 124 -36.74 -39.63 REMARK 500 1 GLU A 125 85.48 -40.83 REMARK 500 2 CYS A 3 -169.46 -111.57 REMARK 500 2 PRO A 5 111.70 -39.93 REMARK 500 2 HIS A 7 124.77 -29.20 REMARK 500 2 PHE A 12 -70.01 -70.62 REMARK 500 2 THR A 32 38.50 -141.68 REMARK 500 2 LEU A 34 -9.39 90.73 REMARK 500 2 THR A 43 -65.10 -97.53 REMARK 500 2 LYS A 47 114.25 173.30 REMARK 500 2 GLN A 50 -61.45 -90.16 REMARK 500 2 LEU A 52 -100.45 -130.03 REMARK 500 2 ALA A 55 -17.82 -38.84 REMARK 500 2 ALA A 65 52.32 -107.93 REMARK 500 2 VAL A 69 -145.59 -74.31 REMARK 500 2 CYS A 70 -67.28 -92.65 REMARK 500 2 TYR A 72 95.29 -69.74 REMARK 500 2 ARG A 75 17.94 -142.72 REMARK 500 2 HIS A 77 2.58 -56.98 REMARK 500 2 THR A 98 -8.46 -59.07 REMARK 500 2 LYS A 118 -36.06 -140.00 REMARK 500 2 CYS A 124 -34.74 -38.82 REMARK 500 2 GLU A 125 90.35 -47.72 REMARK 500 3 HIS A 7 128.60 -28.34 REMARK 500 3 LEU A 17 115.85 -163.08 REMARK 500 3 LEU A 34 -21.26 88.17 REMARK 500 3 THR A 43 -66.33 -90.54 REMARK 500 3 LYS A 47 123.46 171.26 REMARK 500 3 LEU A 52 -92.46 -70.90 REMARK 500 3 ALA A 55 -2.87 -44.20 REMARK 500 3 ALA A 65 55.86 -114.41 REMARK 500 3 SER A 68 41.31 -100.44 REMARK 500 3 TYR A 72 82.72 -167.32 REMARK 500 3 ARG A 75 61.56 -102.45 REMARK 500 REMARK 500 THIS ENTRY HAS 543 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D2B A 1 126 UNP P01033 TIMP1_HUMAN 24 149 SEQRES 1 A 126 CYS THR CYS VAL PRO PRO HIS PRO GLN THR ALA PHE CYS SEQRES 2 A 126 ASN SER ASP LEU VAL ILE ARG ALA LYS PHE VAL GLY THR SEQRES 3 A 126 PRO GLU VAL ASN GLN THR THR LEU TYR GLN ARG TYR GLU SEQRES 4 A 126 ILE LYS MET THR LYS MET TYR LYS GLY PHE GLN ALA LEU SEQRES 5 A 126 GLY ASP ALA ALA ASP ILE ARG PHE VAL TYR THR PRO ALA SEQRES 6 A 126 MET GLU SER VAL CYS GLY TYR PHE HIS ARG SER HIS ASN SEQRES 7 A 126 ARG SER GLU GLU PHE LEU ILE ALA GLY LYS LEU GLN ASP SEQRES 8 A 126 GLY LEU LEU HIS ILE THR THR CYS SER PHE VAL ALA PRO SEQRES 9 A 126 TRP ASN SER LEU SER LEU ALA GLN ARG ARG GLY PHE THR SEQRES 10 A 126 LYS THR TYR THR VAL GLY CYS GLU GLU HELIX 1 1 HIS A 7 SER A 15 1 9 HELIX 2 2 GLY A 48 LEU A 52 5 5 HELIX 3 3 PRO A 104 LEU A 108 5 5 HELIX 4 4 SER A 109 THR A 119 1 11 SHEET 1 A 5 VAL A 102 ALA A 103 0 SHEET 2 A 5 LEU A 84 ALA A 86 -1 N LEU A 84 O ALA A 103 SHEET 3 A 5 VAL A 18 PHE A 23 -1 N ILE A 19 O ILE A 85 SHEET 4 A 5 TYR A 35 LYS A 47 -1 N LYS A 41 O LYS A 22 SHEET 5 A 5 GLU A 28 VAL A 29 -1 N GLU A 28 O ARG A 37 SHEET 1 A1 7 VAL A 102 ALA A 103 0 SHEET 2 A1 7 LEU A 84 ALA A 86 -1 N LEU A 84 O ALA A 103 SHEET 3 A1 7 VAL A 18 PHE A 23 -1 N ILE A 19 O ILE A 85 SHEET 4 A1 7 TYR A 35 LYS A 47 -1 N LYS A 41 O LYS A 22 SHEET 5 A1 7 PHE A 60 PRO A 64 -1 N VAL A 61 O TYR A 38 SHEET 6 A1 7 LEU A 93 HIS A 95 1 O LEU A 94 N TYR A 62 SHEET 7 A1 7 LEU A 89 GLN A 90 -1 N GLN A 90 O LEU A 93 SSBOND 1 CYS A 1 CYS A 70 1555 1555 2.03 SSBOND 2 CYS A 3 CYS A 99 1555 1555 2.02 SSBOND 3 CYS A 13 CYS A 124 1555 1555 2.03 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