HEADER HYDROLASE 01-DEC-07 2JXY TITLE SOLUTION STRUCTURE OF THE HEMOPEXIN-LIKE DOMAIN OF MMP12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEMOPEXIN-LIKE 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS B-SHEET HYDROPHOBIC CORE, CALCIUM, EXTRACELLULAR MATRIX, KEYWDS 2 GLYCOPROTEIN, HYDROLASE, METAL-BINDING, METALLOPROTEASE, KEYWDS 3 POLYMORPHISM, PROTEASE, SECRETED, ZINC, ZYMOGEN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.BERTINI,V.CALDERONE,M.FRAGAI,R.JAISWAL,C.LUCHINAT,M.MELIKIAN REVDAT 4 16-MAR-22 2JXY 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2JXY 1 VERSN REVDAT 2 10-JUN-08 2JXY 1 JRNL REVDAT 1 27-MAY-08 2JXY 0 JRNL AUTH I.BERTINI,V.CALDERONE,M.FRAGAI,R.JAISWAL,C.LUCHINAT, JRNL AUTH 2 M.MELIKIAN,E.MYLONAS,D.I.SVERGUN JRNL TITL EVIDENCE OF RECIPROCAL REORIENTATION OF THE CATALYTIC AND JRNL TITL 2 HEMOPEXIN-LIKE DOMAINS OF FULL-LENGTH MMP-12 JRNL REF J.AM.CHEM.SOC. V. 130 7011 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 18465858 JRNL DOI 10.1021/JA710491Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 20000 STEPS REMARK 4 REMARK 4 2JXY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000100429. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5MM [U-100% 13C; U-100% 15N] REMARK 210 HPX_DOMAIN, 90% H2O, 10% D2O; REMARK 210 0.7MM [U-100% 15N] HPX_DOMAIN, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: ACQUIRED AND PROCESSED USING TOPSPIN SOFTWARE. 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 ILE A 368 H PHE A 371 1.50 REMARK 500 O SER A 367 H SER A 370 1.51 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 ALA A 280 106.59 -41.30 REMARK 500 1 ASP A 283 119.54 -179.04 REMARK 500 1 ASN A 285 42.46 177.68 REMARK 500 1 ASP A 303 -91.08 55.69 REMARK 500 1 LYS A 309 89.04 -168.25 REMARK 500 1 SER A 311 -85.50 64.31 REMARK 500 1 LEU A 324 -74.00 -109.08 REMARK 500 1 PRO A 326 -83.03 -74.96 REMARK 500 1 ALA A 340 -58.29 -155.58 REMARK 500 1 LYS A 348 119.32 -161.82 REMARK 500 1 ASP A 349 -150.94 57.23 REMARK 500 1 ASP A 350 42.17 -87.91 REMARK 500 1 GLU A 361 124.74 -36.41 REMARK 500 1 ASN A 363 61.41 63.45 REMARK 500 1 PHE A 371 71.23 164.68 REMARK 500 1 PHE A 373 96.30 -34.23 REMARK 500 1 PRO A 374 -76.88 -75.06 REMARK 500 1 ASN A 375 -78.80 -96.80 REMARK 500 1 PHE A 376 58.33 -144.70 REMARK 500 1 LYS A 378 -38.28 178.75 REMARK 500 1 PHE A 389 -38.66 -151.30 REMARK 500 1 TYR A 390 31.93 74.08 REMARK 500 1 VAL A 396 74.20 -114.62 REMARK 500 1 ASP A 397 -65.35 75.96 REMARK 500 1 ASN A 398 50.78 -151.43 REMARK 500 1 GLN A 408 29.86 83.09 REMARK 500 1 TYR A 414 63.45 61.16 REMARK 500 1 ILE A 418 -71.35 -69.49 REMARK 500 1 THR A 419 -29.93 -38.07 REMARK 500 1 ASP A 430 -86.85 -75.65 REMARK 500 1 LYS A 436 -160.17 174.62 REMARK 500 1 LYS A 438 49.30 -168.21 REMARK 500 1 SER A 446 33.08 -151.57 REMARK 500 1 LEU A 455 29.97 -163.51 REMARK 500 1 ASN A 465 57.42 -104.07 REMARK 500 2 ALA A 280 96.13 -48.28 REMARK 500 2 ASP A 283 109.33 -176.21 REMARK 500 2 ASN A 285 36.21 -146.21 REMARK 500 2 LYS A 302 70.33 -161.60 REMARK 500 2 ASP A 303 83.15 49.14 REMARK 500 2 ARG A 304 -54.23 76.06 REMARK 500 2 LYS A 309 98.26 -165.01 REMARK 500 2 SER A 311 -75.40 67.20 REMARK 500 2 GLU A 312 77.88 -165.52 REMARK 500 2 SER A 322 -33.90 -37.61 REMARK 500 2 PRO A 326 -90.08 -75.07 REMARK 500 2 SER A 330 -0.05 80.76 REMARK 500 2 ILE A 332 89.60 42.43 REMARK 500 2 ALA A 334 115.84 -168.97 REMARK 500 2 LYS A 348 143.88 -178.53 REMARK 500 REMARK 500 THIS ENTRY HAS 680 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 471 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 289 O REMARK 620 2 GLU A 333 O 99.3 REMARK 620 3 ASP A 381 O 163.0 94.8 REMARK 620 4 ASP A 430 O 97.6 157.6 66.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 471 DBREF 2JXY A 278 470 UNP P39900 MMP12_HUMAN 278 470 SEQADV 2JXY MET A 277 UNP P39900 EXPRESSION TAG SEQRES 1 A 194 MET GLU PRO ALA LEU CYS ASP PRO ASN LEU SER PHE ASP SEQRES 2 A 194 ALA VAL THR THR VAL GLY ASN LYS ILE PHE PHE PHE LYS SEQRES 3 A 194 ASP ARG PHE PHE TRP LEU LYS VAL SER GLU ARG PRO LYS SEQRES 4 A 194 THR SER VAL ASN LEU ILE SER SER LEU TRP PRO THR LEU SEQRES 5 A 194 PRO SER GLY ILE GLU ALA ALA TYR GLU ILE GLU ALA ARG SEQRES 6 A 194 ASN GLN VAL PHE LEU PHE LYS ASP ASP LYS TYR TRP LEU SEQRES 7 A 194 ILE SER ASN LEU ARG PRO GLU PRO ASN TYR PRO LYS SER SEQRES 8 A 194 ILE HIS SER PHE GLY PHE PRO ASN PHE VAL LYS LYS ILE SEQRES 9 A 194 ASP ALA ALA VAL PHE ASN PRO ARG PHE TYR ARG THR TYR SEQRES 10 A 194 PHE PHE VAL ASP ASN GLN TYR TRP ARG TYR ASP GLU ARG SEQRES 11 A 194 ARG GLN MET MET ASP PRO GLY TYR PRO LYS LEU ILE THR SEQRES 12 A 194 LYS ASN PHE GLN GLY ILE GLY PRO LYS ILE ASP ALA VAL SEQRES 13 A 194 PHE TYR SER LYS ASN LYS TYR TYR TYR PHE PHE GLN GLY SEQRES 14 A 194 SER ASN GLN PHE GLU TYR ASP PHE LEU LEU GLN ARG ILE SEQRES 15 A 194 THR LYS THR LEU LYS SER ASN SER TRP PHE GLY CYS HET CA A 471 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 SER A 367 PHE A 371 5 5 HELIX 2 2 LEU A 417 PHE A 422 1 6 SHEET 1 A 4 ALA A 290 VAL A 294 0 SHEET 2 A 4 LYS A 297 LYS A 302 -1 O LYS A 297 N VAL A 294 SHEET 3 A 4 PHE A 305 LEU A 308 -1 O TRP A 307 N PHE A 300 SHEET 4 A 4 ASN A 319 LEU A 320 -1 O ASN A 319 N PHE A 306 SHEET 1 B 3 ALA A 335 ILE A 338 0 SHEET 2 B 3 GLN A 343 LYS A 348 -1 O PHE A 345 N TYR A 336 SHEET 3 B 3 LYS A 351 ILE A 355 -1 O ILE A 355 N VAL A 344 SHEET 1 C 3 ALA A 383 PHE A 385 0 SHEET 2 C 3 ARG A 391 PHE A 394 -1 O TYR A 393 N VAL A 384 SHEET 3 C 3 TYR A 403 ASP A 404 -1 O TYR A 403 N THR A 392 SHEET 1 D 4 ALA A 431 PHE A 433 0 SHEET 2 D 4 TYR A 440 PHE A 443 -1 O TYR A 441 N PHE A 433 SHEET 3 D 4 GLN A 448 TYR A 451 -1 O PHE A 449 N PHE A 442 SHEET 4 D 4 THR A 461 LEU A 462 -1 O LEU A 462 N GLN A 448 SSBOND 1 CYS A 282 CYS A 470 1555 1555 2.31 LINK O ASP A 289 CA CA A 471 1555 1555 1.82 LINK O GLU A 333 CA CA A 471 1555 1555 2.67 LINK O ASP A 381 CA CA A 471 1555 1555 1.66 LINK O ASP A 430 CA CA A 471 1555 1555 2.92 SITE 1 AC1 3 PHE A 288 ASP A 289 GLU A 333 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 MODEL 1