PDB Short entry for 3CI7 HEADER HYDROLASE INHIBITOR 11-MAR-08 3CI7 TITLE CRYSTAL STRUCTURE OF A SIMPLIFIED BPTI CONTAINING 20 ALANINES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BOVINE PANCREATIC TRYPSIN INHIBITOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: BPTI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PEPTIDE SYNTHESIS KEYWDS SEQUENCE SIMPLIFICATION, BOVINE PANCREATIC TRYPSIN INHIBITOR, KEYWDS 2 HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR M.M.ISLAM,S.SOHYA,K.NOGUCHI,M.YOHDA,Y.KURODA REVDAT 3 01-NOV-23 3CI7 1 REMARK REVDAT 2 24-FEB-09 3CI7 1 VERSN REVDAT 1 21-OCT-08 3CI7 0 JRNL AUTH M.M.ISLAM,S.SOHYA,K.NOGUCHI,M.YOHDA,Y.KURODA JRNL TITL CRYSTAL STRUCTURE OF AN EXTENSIVELY SIMPLIFIED VARIANT OF JRNL TITL 2 BOVINE PANCREATIC TRYPSIN INHIBITOR IN WHICH OVER ONE-THIRD JRNL TITL 3 OF THE RESIDUES ARE ALANINES JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 15334 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18829434 JRNL DOI 10.1073/PNAS.0802699105 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 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) : 0.157 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.151 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2047 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 40883 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.157 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.151 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.240 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1891 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 36064 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1643 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 277 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 : 2 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) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL 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 3CI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 44.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 5PTI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, PH8.7, LITHIUM SULFATE, REMARK 280 PEG4000, VAPOR DIFFUSION, HANGING 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 24.75400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.92450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.61100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.92450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.75400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.61100 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA B 57 REMARK 465 ALA B 58 REMARK 465 ALA D 58 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 15 CD CE NZ REMARK 470 ARG A 39 CD NE CZ NH1 NH2 REMARK 470 LYS B 15 CG CD CE NZ REMARK 470 ARG B 39 CD NE CZ NH1 NH2 REMARK 470 ARG D 39 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 41 NZ 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 17 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 42 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG C 1 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG D 1 CD - NE - CZ ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG D 1 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG D 17 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 6002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 6004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZJX RELATED DB: PDB DBREF 3CI7 A 1 58 PDB 3CI7 3CI7 1 58 DBREF 3CI7 B 1 58 PDB 3CI7 3CI7 1 58 DBREF 3CI7 C 1 58 PDB 3CI7 3CI7 1 58 DBREF 3CI7 D 1 58 PDB 3CI7 3CI7 1 58 SEQRES 1 A 58 ARG PRO ALA PHE CYS LEU GLU PRO PRO TYR ALA GLY PRO SEQRES 2 A 58 GLY LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA ALA SEQRES 3 A 58 ALA GLY ALA ALA GLN ALA PHE VAL TYR GLY GLY ALA ARG SEQRES 4 A 58 ALA LYS ARG ASN ASN PHE ALA SER ALA ALA ASP ALA LEU SEQRES 5 A 58 ALA ALA CYS ALA ALA ALA SEQRES 1 B 58 ARG PRO ALA PHE CYS LEU GLU PRO PRO TYR ALA GLY PRO SEQRES 2 B 58 GLY LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA ALA SEQRES 3 B 58 ALA GLY ALA ALA GLN ALA PHE VAL TYR GLY GLY ALA ARG SEQRES 4 B 58 ALA LYS ARG ASN ASN PHE ALA SER ALA ALA ASP ALA LEU SEQRES 5 B 58 ALA ALA CYS ALA ALA ALA SEQRES 1 C 58 ARG PRO ALA PHE CYS LEU GLU PRO PRO TYR ALA GLY PRO SEQRES 2 C 58 GLY LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA ALA SEQRES 3 C 58 ALA GLY ALA ALA GLN ALA PHE VAL TYR GLY GLY ALA ARG SEQRES 4 C 58 ALA LYS ARG ASN ASN PHE ALA SER ALA ALA ASP ALA LEU SEQRES 5 C 58 ALA ALA CYS ALA ALA ALA SEQRES 1 D 58 ARG PRO ALA PHE CYS LEU GLU PRO PRO TYR ALA GLY PRO SEQRES 2 D 58 GLY LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA ALA SEQRES 3 D 58 ALA GLY ALA ALA GLN ALA PHE VAL TYR GLY GLY ALA ARG SEQRES 4 D 58 ALA LYS ARG ASN ASN PHE ALA SER ALA ALA ASP ALA LEU SEQRES 5 D 58 ALA ALA CYS ALA ALA ALA HET SO4 A6001 5 HET SO4 A6003 5 HET SO4 B6004 5 HET SO4 D6002 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 HOH *277(H2 O) HELIX 1 1 PRO A 2 GLU A 7 5 6 HELIX 2 2 SER A 47 ALA A 56 1 10 HELIX 3 3 PRO B 2 GLU B 7 5 6 HELIX 4 4 SER B 47 ALA B 56 1 10 HELIX 5 5 PRO C 2 GLU C 7 5 6 HELIX 6 6 SER C 47 ALA C 56 1 10 HELIX 7 7 PRO D 2 GLU D 7 5 6 HELIX 8 8 SER D 47 CYS D 55 1 9 SHEET 1 A 2 ILE A 18 ASN A 24 0 SHEET 2 A 2 ALA A 29 TYR A 35 -1 O TYR A 35 N ILE A 18 SHEET 1 B 2 ILE B 18 ASN B 24 0 SHEET 2 B 2 ALA B 29 TYR B 35 -1 O TYR B 35 N ILE B 18 SHEET 1 C 2 ILE C 18 ASN C 24 0 SHEET 2 C 2 ALA C 29 TYR C 35 -1 O TYR C 35 N ILE C 18 SHEET 1 D 2 ILE D 18 ASN D 24 0 SHEET 2 D 2 ALA D 29 TYR D 35 -1 O ALA D 29 N ASN D 24 SSBOND 1 CYS A 5 CYS A 55 1555 1555 2.07 SSBOND 2 CYS B 5 CYS B 55 1555 1555 2.04 SSBOND 3 CYS C 5 CYS C 55 1555 1555 2.08 SSBOND 4 CYS D 5 CYS D 55 1555 1555 2.05 SITE 1 AC1 4 ARG A 20 TYR A 35 GLY A 37 ALA A 40 SITE 1 AC2 2 ARG B 42 ARG D 20 SITE 1 AC3 5 ALA A 30 GLN A 31 ALA A 32 TYR B 21 SITE 2 AC3 5 GLN D 31 SITE 1 AC4 4 ARG B 20 TYR B 35 ALA B 40 ARG D 42 CRYST1 49.508 57.222 71.849 90.00 90.00 90.00 P 21 21 21 16 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 0.020199 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013918 0.00000