HEADER HYDROLASE 07-MAR-13 4JIU TITLE CRYSTAL STRUCTURE OF THE METALLOPEPTIDASE ZYMOGEN OF PYROCOCCUS ABYSSI TITLE 2 ABYLYSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROABYLYSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 STRAIN: GE5 / ORSAY; SOURCE 5 GENE: PAB3079, PYRAB02920; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS HYDROLASE, METALLOPEPTIDASE ZYMOGEN, MINIGLUZINCIN EXPDTA X-RAY DIFFRACTION AUTHOR M.LOPEZ-PELEGRIN,N.CERDA-COSTA,F.MARTINEZ-JIMENEZ,A.CINTAS-PEDROLA, AUTHOR 2 A.CANALS,J.R.PEINADO,M.A.MARTI-RENOM,C.LOPEZ-OTIN,J.L.AROLAS, AUTHOR 3 F.X.GOMIS-RUTH REVDAT 4 20-MAR-24 4JIU 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4JIU 1 COMPND REMARK REVDAT 2 04-SEP-13 4JIU 1 JRNL REVDAT 1 12-JUN-13 4JIU 0 JRNL AUTH M.LOPEZ-PELEGRIN,N.CERDA-COSTA,F.MARTINEZ-JIMENEZ, JRNL AUTH 2 A.CINTAS-PEDROLA,A.CANALS,J.R.PEINADO,M.A.MARTI-RENOM, JRNL AUTH 3 C.LOPEZ-OTIN,J.L.AROLAS,F.X.GOMIS-RUTH JRNL TITL A NOVEL FAMILY OF SOLUBLE MINIMAL SCAFFOLDS PROVIDES JRNL TITL 2 STRUCTURAL INSIGHT INTO THE CATALYTIC DOMAINS OF INTEGRAL JRNL TITL 3 MEMBRANE METALLOPEPTIDASES JRNL REF J.BIOL.CHEM. V. 288 21279 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23733187 JRNL DOI 10.1074/JBC.M113.476580 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.147 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 778 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 39668 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 872 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 8 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 2.240 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9540,1.2821 REMARK 200 MONOCHROMATOR : SI(311) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 44.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07200 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) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 18.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 0.2M SODIUM/POTASSIUM REMARK 280 PHOSPHATE, 2.6M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.31000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.31000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.33000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 ASP A 11 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 22 CG - CD - NE ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 TYR A 56 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 102 NH1 - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 60 NE2 REMARK 620 2 HIS A 64 NE2 107.1 REMARK 620 3 HIS A 72 NE2 104.1 104.2 REMARK 620 4 VAL A 105 O 121.3 113.0 105.4 REMARK 620 5 VAL A 105 OXT 86.6 91.3 157.3 52.5 REMARK 620 N 1 2 3 4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JIX RELATED DB: PDB DBREF 4JIU A 1 105 UNP Q9V1Y2 Q9V1Y2_PYRAB 1 105 SEQADV 4JIU VAL A 2 UNP Q9V1Y2 LEU 2 ENGINEERED MUTATION SEQRES 1 A 105 MET VAL GLU ASP LEU LEU GLU HIS ALA LYS ASP ILE LEU SEQRES 2 A 105 GLY TYR GLN ARG PRO VAL LYS VAL ARG ILE ARG PRO LEU SEQRES 3 A 105 LYS MET SER ILE ALA ARG VAL SER PHE LYS TYR GLY THR SEQRES 4 A 105 ILE THR LEU ASP PRO ALA VAL LEU ASN LEU GLU GLU GLU SEQRES 5 A 105 GLU MET PHE TYR ILE LEU ILE HIS GLU LEU ALA HIS LEU SEQRES 6 A 105 LYS ALA GLU THR SER TYR HIS SER SER SER PHE TRP ARG SEQRES 7 A 105 GLU VAL GLU LYS VAL PHE PRO GLY GLU ARG ALA LYS GLU SEQRES 8 A 105 ILE GLU ASP ARG ILE MET THR LYS LEU GLN ARG ASN MET SEQRES 9 A 105 VAL HET ZN A 201 1 HET GOL A 202 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *147(H2 O) HELIX 1 1 MET A 1 GLY A 14 1 14 HELIX 2 2 PRO A 44 LEU A 49 5 6 HELIX 3 3 GLU A 50 GLU A 68 1 19 HELIX 4 4 SER A 73 GLU A 81 1 9 HELIX 5 5 GLU A 87 GLN A 101 1 15 SHEET 1 A 3 LYS A 20 ILE A 23 0 SHEET 2 A 3 THR A 39 LEU A 42 1 O LEU A 42 N ARG A 22 SHEET 3 A 3 ALA A 31 SER A 34 -1 N ARG A 32 O THR A 41 LINK NE2 HIS A 60 ZN ZN A 201 1555 1555 1.98 LINK NE2 HIS A 64 ZN ZN A 201 1555 1555 2.00 LINK NE2 HIS A 72 ZN ZN A 201 1555 1555 2.02 LINK O VAL A 105 ZN ZN A 201 1555 1555 2.02 LINK OXT VAL A 105 ZN ZN A 201 1555 1555 2.69 SITE 1 AC1 4 HIS A 60 HIS A 64 HIS A 72 VAL A 105 SITE 1 AC2 6 TRP A 77 HOH A 312 HOH A 319 HOH A 388 SITE 2 AC2 6 HOH A 389 HOH A 392 CRYST1 34.620 44.660 72.000 90.00 90.00 90.00 P 21 21 21 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 0.028885 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013889 0.00000