HEADER HYDROLASE 03-JUL-02 1M4L TITLE STRUCTURE OF NATIVE CARBOXYPEPTIDASE A AT 1.25 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBOXYPEPTIDASE A; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.17.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: PANCREAS KEYWDS CARBOXYPEPTIDASE A, METALLOPROTEINASE, METALLOEXOPROTEINASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KILSHTAIN-VARDI,M.GLICK,H.M.GREENBLATT,A.GOLDBLUM,G.SHOHAM REVDAT 4 25-OCT-23 1M4L 1 REMARK LINK REVDAT 3 24-FEB-09 1M4L 1 VERSN REVDAT 2 04-MAR-03 1M4L 1 JRNL REVDAT 1 10-JAN-03 1M4L 0 JRNL AUTH A.KILSHTAIN-VARDI,M.GLICK,H.M.GREENBLATT,A.GOLDBLUM,G.SHOHAM JRNL TITL REFINED STRUCTURE OF BOVINE CARBOXYPEPTIDASE A AT 1.25 A JRNL TITL 2 RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 323 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12554943 JRNL DOI 10.1107/S0907444902015706 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.104 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3416 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 64976 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.099 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3103 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 58913 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2436 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 375 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2764.4 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 9 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 25563 REMARK 3 NUMBER OF RESTRAINTS : 31254 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.076 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.080 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.056 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.102 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 0.05. REMARK 4 REMARK 4 1M4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 297 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.085 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64976 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 36.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: PDB ENTERY 1YME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.13350 REMARK 290 SMTRY3 2 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 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 ARG A 2 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU A 15 CB - CG - CD2 ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP A 16 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 TYR A 19 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP A 20 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 40 NH1 - CZ - NH2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 59 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 PHE A 82 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 PHE A 82 CB - CG - CD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 PHE A 86 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 89 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 127 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG A 127 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 THR A 133 N - CA - CB ANGL. DEV. = 11.7 DEGREES REMARK 500 TYR A 238 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 276 CD - NE - CZ ANGL. DEV. = 23.7 DEGREES REMARK 500 ARG A 276 NE - CZ - NH1 ANGL. DEV. = 6.1 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 GLN A 122 -42.53 -132.74 REMARK 500 SER A 199 -11.25 147.25 REMARK 500 GLN A 200 62.22 64.94 REMARK 500 ILE A 247 -86.08 -114.62 REMARK 500 ASP A 273 -149.35 -107.03 REMARK 500 LEU A 280 50.11 -97.84 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 A1308 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 ND1 REMARK 620 2 GLU A 72 OE1 119.4 REMARK 620 3 GLU A 72 OE2 93.3 56.5 REMARK 620 4 HIS A 196 ND1 101.3 94.8 151.3 REMARK 620 5 HOH A1324 O 118.4 114.9 93.6 100.9 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 1308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YME RELATED DB: PDB REMARK 900 1YME CONTAINS THE SAME PROTEIN AT 1.53 RESOLUTION. REMARK 900 RELATED ID: 2CTB RELATED DB: PDB REMARK 900 2CTB CONTAINS THE SAME PROTEIN AT 1.5 RESOLUTION. REMARK 900 RELATED ID: 5CPA RELATED DB: PDB REMARK 900 5CPA CONTAINS THE SAME PROTEIN AT 1.54 RESOLUTION. DBREF 1M4L A 1 307 UNP P00730 CBPA1_BOVIN 111 417 SEQADV 1M4L ALA A 228 UNP P00730 GLU 338 SEE REMARK 999 SEQADV 1M4L VAL A 305 UNP P00730 LEU 415 SEE REMARK 999 SEQRES 1 A 307 ALA ARG SER THR ASN THR PHE ASN TYR ALA THR TYR HIS SEQRES 2 A 307 THR LEU ASP GLU ILE TYR ASP PHE MET ASP LEU LEU VAL SEQRES 3 A 307 ALA GLU HIS PRO GLN LEU VAL SER LYS LEU GLN ILE GLY SEQRES 4 A 307 ARG SER TYR GLU GLY ARG PRO ILE TYR VAL LEU LYS PHE SEQRES 5 A 307 SER THR GLY GLY SER ASN ARG PRO ALA ILE TRP ILE ASP SEQRES 6 A 307 LEU GLY ILE HIS SER ARG GLU TRP ILE THR GLN ALA THR SEQRES 7 A 307 GLY VAL TRP PHE ALA LYS LYS PHE THR GLU ASP TYR GLY SEQRES 8 A 307 GLN ASP PRO SER PHE THR ALA ILE LEU ASP SER MET ASP SEQRES 9 A 307 ILE PHE LEU GLU ILE VAL THR ASN PRO ASP GLY PHE ALA SEQRES 10 A 307 PHE THR HIS SER GLN ASN ARG LEU TRP ARG LYS THR ARG SEQRES 11 A 307 SER VAL THR SER SER SER LEU CYS VAL GLY VAL ASP ALA SEQRES 12 A 307 ASN ARG ASN TRP ASP ALA GLY PHE GLY LYS ALA GLY ALA SEQRES 13 A 307 SER SER SER PRO CYS SER GLU THR TYR HIS GLY LYS TYR SEQRES 14 A 307 ALA ASN SER GLU VAL GLU VAL LYS SER ILE VAL ASP PHE SEQRES 15 A 307 VAL LYS ASP HIS GLY ASN PHE LYS ALA PHE LEU SER ILE SEQRES 16 A 307 HIS SER TYR SER GLN LEU LEU LEU TYR PRO TYR GLY TYR SEQRES 17 A 307 THR THR GLN SER ILE PRO ASP LYS THR GLU LEU ASN GLN SEQRES 18 A 307 VAL ALA LYS SER ALA VAL ALA ALA LEU LYS SER LEU TYR SEQRES 19 A 307 GLY THR SER TYR LYS TYR GLY SER ILE ILE THR THR ILE SEQRES 20 A 307 TYR GLN ALA SER GLY GLY SER ILE ASP TRP SER TYR ASN SEQRES 21 A 307 GLN GLY ILE LYS TYR SER PHE THR PHE GLU LEU ARG ASP SEQRES 22 A 307 THR GLY ARG TYR GLY PHE LEU LEU PRO ALA SER GLN ILE SEQRES 23 A 307 ILE PRO THR ALA GLN GLU THR TRP LEU GLY VAL LEU THR SEQRES 24 A 307 ILE MET GLU HIS THR VAL ASN ASN HET ZN A1308 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *375(H2 O) HELIX 1 1 THR A 14 HIS A 29 1 16 HELIX 2 2 GLU A 72 TYR A 90 1 19 HELIX 3 3 ASP A 93 MET A 103 1 11 HELIX 4 4 ASN A 112 GLN A 122 1 11 HELIX 5 5 ASP A 142 ASN A 146 5 5 HELIX 6 6 GLU A 173 GLY A 187 1 15 HELIX 7 7 ASP A 215 SER A 232 1 18 HELIX 8 8 ILE A 243 ILE A 247 1 5 HELIX 9 9 GLY A 253 GLN A 261 1 9 HELIX 10 10 PRO A 282 SER A 284 5 3 HELIX 11 11 GLN A 285 ASN A 307 1 23 SHEET 1 A 8 VAL A 33 ARG A 40 0 SHEET 2 A 8 PRO A 46 PHE A 52 -1 O VAL A 49 N LEU A 36 SHEET 3 A 8 ASP A 104 GLU A 108 -1 O ILE A 105 N PHE A 52 SHEET 4 A 8 ALA A 61 LEU A 66 1 N ILE A 64 O GLU A 108 SHEET 5 A 8 PHE A 189 HIS A 196 1 O LYS A 190 N ALA A 61 SHEET 6 A 8 TYR A 265 GLU A 270 1 O PHE A 269 N HIS A 196 SHEET 7 A 8 LEU A 201 TYR A 204 -1 N LEU A 203 O THR A 268 SHEET 8 A 8 LYS A 239 SER A 242 1 O LYS A 239 N LEU A 202 SSBOND 1 CYS A 138 CYS A 161 1555 1555 1.97 LINK ND1 HIS A 69 ZN ZN A1308 1555 1555 2.04 LINK OE1 GLU A 72 ZN ZN A1308 1555 1555 2.27 LINK OE2 GLU A 72 ZN ZN A1308 1555 1555 2.25 LINK ND1 HIS A 196 ZN ZN A1308 1555 1555 2.05 LINK ZN ZN A1308 O HOH A1324 1555 1555 1.96 CISPEP 1 SER A 197 TYR A 198 0 -9.98 CISPEP 2 PRO A 205 TYR A 206 0 -0.12 CISPEP 3 ARG A 272 ASP A 273 0 -3.50 SITE 1 AC1 4 HIS A 69 GLU A 72 HIS A 196 HOH A1324 CRYST1 51.687 60.267 47.453 90.00 97.47 90.00 P 1 21 1 2 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 0.019347 0.000000 0.002537 0.00000 SCALE2 0.000000 0.016593 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021254 0.00000