PDB Short entry for 2POJ HEADER HYDROLASE 26-APR-07 2POJ TITLE NMR SOLUTION STRUCTURE OF THE INHIBITOR-FREE STATE OF MACROPHAGE TITLE 2 METALLOELASTASE (MMP-12) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: HME, MATRIX METALLOPROTEINASE-12, MMP-12, MACROPHAGE COMPND 6 ELASTASE, ME; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP12, HME; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET 21A KEYWDS INHIBITOR-FREE SOLUTION STRUCTURE, MATRIX METALOPROTEINASE, KEYWDS 2 MACROPHAGE METALLOELASTASE, MMP-12, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.BHASKARAN,S.R.VAN DOREN REVDAT 3 20-OCT-21 2POJ 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2POJ 1 VERSN REVDAT 1 04-DEC-07 2POJ 0 JRNL AUTH R.BHASKARAN,M.O.PALMIER,N.A.BAGEGNI,X.LIANG,S.R.VAN DOREN JRNL TITL SOLUTION STRUCTURE OF INHIBITOR-FREE HUMAN METALLOELASTASE JRNL TITL 2 (MMP-12) INDICATES AN INTERNAL CONFORMATIONAL ADJUSTMENT. JRNL REF J.MOL.BIOL. V. 374 1333 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17997411 JRNL DOI 10.1016/J.JMB.2007.10.028 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, CYANA 2.1 REMARK 3 AUTHORS : VARIAN ASSOCIATES (VNMR), GUENTERT, P (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2813 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS AND 220 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 2POJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042608. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 299 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 20MM IMIDAZOLE,10MM CACL2 AND REMARK 210 20UM ZNCL2 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1. UNIFORM LABELING WITH 15N: U REMARK 210 -15N 20MM IMIDAZOLE; 10MM CACL2; REMARK 210 20 UM ZNCL2; 90% H2O, 10% D2O; REMARK 210 2. UNIFORM LABELING WITH 13C, REMARK 210 15N: U-15N,13C 20MM IMIDAZOLE ; REMARK 210 10MM CACL2; 20 UM ZNCL2; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNCA-J REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.6, SPARKY 3.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS, AUTOMATED REMARK 210 ANALYSIS OF NOESY DATA AND 3D REMARK 210 STRUCTURES. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY AND AUTOMATED ANALYSIS OF 3D STRUCTURE. REMARK 210 REMARK 210 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION NMR REMARK 210 DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND SCALE REMARK 210 RECORDS BE INCLUDED, BUT THE VALUES ON THESE RECORDS ARE REMARK 210 MEANINGLESS. 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 O SER A 189 H ILE A 191 1.56 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 GLU A 102 143.23 175.88 REMARK 500 1 PRO A 104 78.06 -69.79 REMARK 500 1 PRO A 146 30.59 -69.78 REMARK 500 1 THR A 154 50.66 -159.78 REMARK 500 1 ALA A 173 99.59 50.43 REMARK 500 1 PHE A 174 -170.91 -58.72 REMARK 500 1 LYS A 177 132.85 -33.77 REMARK 500 1 ILE A 180 97.64 -49.92 REMARK 500 1 PHE A 185 -152.93 -105.60 REMARK 500 1 PRO A 187 52.33 -69.78 REMARK 500 1 THR A 210 96.93 -66.65 REMARK 500 1 LYS A 233 17.36 -143.03 REMARK 500 2 ARG A 101 38.20 39.09 REMARK 500 2 PRO A 123 0.86 -69.73 REMARK 500 2 PRO A 146 30.36 -69.76 REMARK 500 2 THR A 154 52.96 -153.48 REMARK 500 2 ALA A 173 99.39 50.45 REMARK 500 2 PHE A 174 -171.23 -58.22 REMARK 500 2 LYS A 177 132.02 -33.34 REMARK 500 2 ILE A 180 97.66 -49.89 REMARK 500 2 PHE A 185 -148.71 -104.63 REMARK 500 2 PRO A 187 51.87 -69.79 REMARK 500 2 THR A 210 97.51 -66.78 REMARK 500 2 LYS A 233 19.81 -143.47 REMARK 500 2 ARG A 249 133.37 -177.19 REMARK 500 3 GLU A 102 130.24 177.75 REMARK 500 3 PRO A 107 71.95 -69.89 REMARK 500 3 VAL A 108 141.78 -38.60 REMARK 500 3 PRO A 146 30.53 -69.78 REMARK 500 3 THR A 154 53.25 -153.34 REMARK 500 3 PHE A 171 40.34 72.80 REMARK 500 3 HIS A 172 -41.65 -135.72 REMARK 500 3 ALA A 173 99.93 54.31 REMARK 500 3 PHE A 174 -168.27 -60.72 REMARK 500 3 LYS A 177 134.52 -35.29 REMARK 500 3 ILE A 180 96.27 -50.13 REMARK 500 3 PHE A 185 -138.93 -99.43 REMARK 500 3 PRO A 187 59.54 -69.83 REMARK 500 3 THR A 210 97.43 -66.74 REMARK 500 3 PRO A 232 0.25 -69.62 REMARK 500 3 LYS A 233 25.42 -143.05 REMARK 500 3 ARG A 249 134.08 -171.23 REMARK 500 4 ARG A 101 59.67 36.59 REMARK 500 4 GLU A 102 132.87 178.09 REMARK 500 4 MET A 103 150.41 -49.96 REMARK 500 4 VAL A 108 -174.38 -57.08 REMARK 500 4 PRO A 146 30.10 -69.78 REMARK 500 4 THR A 154 61.57 -154.31 REMARK 500 4 PHE A 171 40.24 72.80 REMARK 500 4 HIS A 172 -41.17 -135.58 REMARK 500 REMARK 500 THIS ENTRY HAS 339 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 268 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD1 REMARK 620 2 ASP A 124 OD2 47.7 REMARK 620 3 GLU A 199 O 119.8 75.1 REMARK 620 4 GLU A 199 OE2 95.0 85.3 58.3 REMARK 620 5 GLU A 201 O 99.2 61.6 59.6 114.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 267 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 158 O REMARK 620 2 GLY A 190 O 158.9 REMARK 620 3 GLY A 192 O 55.7 138.1 REMARK 620 4 ASP A 194 OD1 94.2 106.2 65.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 265 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 168 NE2 REMARK 620 2 ASP A 170 OD2 128.9 REMARK 620 3 HIS A 183 NE2 132.2 87.4 REMARK 620 4 HIS A 196 ND1 133.2 75.2 79.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 266 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD1 REMARK 620 2 GLY A 176 O 79.3 REMARK 620 3 GLY A 178 O 57.8 59.1 REMARK 620 4 ILE A 180 O 92.8 151.6 137.7 REMARK 620 5 ASP A 198 OD2 118.1 60.0 118.3 101.9 REMARK 620 6 GLU A 201 OE2 143.3 92.2 87.1 109.3 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 264 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 218 NE2 REMARK 620 2 HIS A 222 NE2 87.6 REMARK 620 3 HIS A 228 NE2 154.4 93.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 268 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7089 RELATED DB: BMRB REMARK 900 NMR CHEMICAL SHIFT ASSIGNMENT DATA REMARK 900 RELATED ID: 2OXU RELATED DB: PDB REMARK 900 INHIBITOR REMOVED XRAY STRUCTURE OF MMP12 REMARK 900 RELATED ID: 1JK3 RELATED DB: PDB REMARK 900 INHIBITOR BOUND XRAY STRUCTURE REMARK 900 RELATED ID: 1JIZ RELATED DB: PDB REMARK 900 INHIBITOR BOUND XRAY STRUCTURE DBREF 2POJ A 100 263 UNP P39900 MMP12_HUMAN 100 263 SEQADV 2POJ ALA A 219 UNP P39900 GLU 219 ENGINEERED MUTATION SEQRES 1 A 164 PHE ARG GLU MET PRO GLY GLY PRO VAL TRP ARG LYS HIS SEQRES 2 A 164 TYR ILE THR TYR ARG ILE ASN ASN TYR THR PRO ASP MET SEQRES 3 A 164 ASN ARG GLU ASP VAL ASP TYR ALA ILE ARG LYS ALA PHE SEQRES 4 A 164 GLN VAL TRP SER ASN VAL THR PRO LEU LYS PHE SER LYS SEQRES 5 A 164 ILE ASN THR GLY MET ALA ASP ILE LEU VAL VAL PHE ALA SEQRES 6 A 164 ARG GLY ALA HIS GLY ASP PHE HIS ALA PHE ASP GLY LYS SEQRES 7 A 164 GLY GLY ILE LEU ALA HIS ALA PHE GLY PRO GLY SER GLY SEQRES 8 A 164 ILE GLY GLY ASP ALA HIS PHE ASP GLU ASP GLU PHE TRP SEQRES 9 A 164 THR THR HIS SER GLY GLY THR ASN LEU PHE LEU THR ALA SEQRES 10 A 164 VAL HIS ALA ILE GLY HIS SER LEU GLY LEU GLY HIS SER SEQRES 11 A 164 SER ASP PRO LYS ALA VAL MET PHE PRO THR TYR LYS TYR SEQRES 12 A 164 VAL ASP ILE ASN THR PHE ARG LEU SER ALA ASP ASP ILE SEQRES 13 A 164 ARG GLY ILE GLN SER LEU TYR GLY HET ZN A 264 1 HET ZN A 265 1 HET CA A 266 1 HET CA A 267 1 HET CA A 268 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 3(CA 2+) HELIX 1 1 ASN A 126 GLN A 139 1 14 HELIX 2 2 ASN A 211 GLY A 225 1 15 HELIX 3 3 SER A 251 GLY A 263 1 13 SHEET 1 A 3 LYS A 148 LYS A 151 0 SHEET 2 A 3 TYR A 113 ILE A 118 1 N ILE A 114 O LYS A 148 SHEET 3 A 3 ILE A 159 VAL A 161 1 O ILE A 159 N THR A 115 SHEET 1 B 2 ALA A 182 HIS A 183 0 SHEET 2 B 2 HIS A 196 PHE A 197 -1 O HIS A 196 N HIS A 183 LINK OD1 ASP A 124 CA CA A 268 1555 1555 2.77 LINK OD2 ASP A 124 CA CA A 268 1555 1555 2.66 LINK O ASP A 158 CA CA A 267 1555 1555 2.55 LINK NE2 HIS A 168 ZN ZN A 265 1555 1555 2.14 LINK OD2 ASP A 170 ZN ZN A 265 1555 1555 2.06 LINK OD1 ASP A 175 CA CA A 266 1555 1555 2.60 LINK O GLY A 176 CA CA A 266 1555 1555 2.49 LINK O GLY A 178 CA CA A 266 1555 1555 2.57 LINK O ILE A 180 CA CA A 266 1555 1555 2.53 LINK NE2 HIS A 183 ZN ZN A 265 1555 1555 2.11 LINK O GLY A 190 CA CA A 267 1555 1555 2.58 LINK O GLY A 192 CA CA A 267 1555 1555 2.53 LINK OD1 ASP A 194 CA CA A 267 1555 1555 2.61 LINK ND1 HIS A 196 ZN ZN A 265 1555 1555 2.29 LINK OD2 ASP A 198 CA CA A 266 1555 1555 2.64 LINK O GLU A 199 CA CA A 268 1555 1555 2.57 LINK OE2 GLU A 199 CA CA A 268 1555 1555 2.64 LINK OE2 GLU A 201 CA CA A 266 1555 1555 2.49 LINK O GLU A 201 CA CA A 268 1555 1555 2.66 LINK NE2 HIS A 218 ZN ZN A 264 1555 1555 2.21 LINK NE2 HIS A 222 ZN ZN A 264 1555 1555 2.22 LINK NE2 HIS A 228 ZN ZN A 264 1555 1555 2.21 SITE 1 AC1 3 HIS A 218 HIS A 222 HIS A 228 SITE 1 AC2 5 HIS A 168 ASP A 170 HIS A 172 HIS A 183 SITE 2 AC2 5 HIS A 196 SITE 1 AC3 7 ASP A 175 GLY A 176 GLY A 178 GLY A 179 SITE 2 AC3 7 ILE A 180 ASP A 198 GLU A 201 SITE 1 AC4 6 ALA A 157 ASP A 158 GLY A 190 ILE A 191 SITE 2 AC4 6 GLY A 192 ASP A 194 SITE 1 AC5 4 ASP A 124 GLU A 199 ASP A 200 GLU A 201 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