10 20 30 40 50 60 70 80 2ZVX - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE INHIBITOR 24-NOV-08 2ZVX
TITLE STRUCTURE OF A BPTI-[5,55] VARIANT CONTAINING GLY/VAL AT THE TITLE 2 14/38TH POSITIONS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANCREATIC TRYPSIN INHIBITOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PROTEIN FOLDING, PROTEIN STABILIZATION, PROTEIN DESIGN, KEYWDS 2 PHARMACEUTICAL, PROTEASE INHIBITOR, SECRETED, SERINE KEYWDS 3 PROTEASE INHIBITOR, HYDROLASE INHIBITOR, DISULFIDE BOND
EXPDTA X-RAY DIFFRACTION
AUTHOR M.M.ISLAM,S.SOHYA,K.NOGUCHI,M.YOHDA,Y.KURODA
REVDAT 2 27-OCT-09 2ZVX 1 DBREF REVDAT 1 13-OCT-09 2ZVX 0
JRNL AUTH M.M.ISLAM,S.SOHYA,K.NOGUCHI,S.KIDOKORO,M.YOHDA, JRNL AUTH 2 Y.KURODA JRNL TITL THERMODYNAMIC AND STRUCTURAL ANALYSIS OF HIGHLY JRNL TITL 2 STABILIZED BPTIS BY SINGLE AND DOUBLE MUTATIONS JRNL REF PROTEINS V. 77 962 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19830687 JRNL DOI 10.1002/PROT.22522
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.09 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) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.179 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1861 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 35190 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)) : 0.170 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1667 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31348 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 885 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 985.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8342 REMARK 3 NUMBER OF RESTRAINTS : 11036 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.081 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.081 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.016 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.035 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.070 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 2ZVX COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-08. REMARK 100 THE RCSB ID CODE IS RCSB028492.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35190 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 53.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.05200 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) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.04200 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 2ZJX REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PH8.5, 0.2M LITHIUM REMARK 280 CHLORIDE, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K
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 20.42200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 B 15 NZ REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 ARG B 53 CG CD NE CZ NH1 NH2
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 1 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 1 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 17 CD - NE - CZ ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG B 17 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 17 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 20 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 42 CD - NE - CZ ANGL. DEV. = 9.0 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 4001 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 4002 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 4003
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZJX RELATED DB: PDB REMARK 900 BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) CONTAINING ONLY REMARK 900 THE [5,55] DISULFIDE BONDD REMARK 900 RELATED ID: 3CI7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SIMPLIFIED BPTI CONTAINING 20 REMARK 900 ALANINES
REMARK 999 REMARK 999 SEQUENCE REMARK 999 NATIVELY FOLDED BPTI VARIANT ENGINEREED FROM THE WILD TYPE BPTI. REMARK 999 THIS BPTI HAS A SINGLE DISSULFIDE BOND BETWEEN RESIDUE 5 AND 55, REMARK 999 THE OTHER CYSTEINES BEING MUTATED TO A, G OR V. ADDITIONALLY, REMARK 999 M52 WAS MUTATED TO L FOR PURIFICATION PURPOSE. THIS BPTI REMARK 999 SEQUENCE CONTAINS A TOTAL OF 5 MUTATIONS (C14G, C30A, C38V, M52L REMARK 999 AND C51A) WITH RESPECT TO THE WILD-TYPE SEQUENCE.
DBREF 2ZVX A 1 58 UNP P00974 BPT1_BOVIN 36 93 DBREF 2ZVX B 1 58 UNP P00974 BPT1_BOVIN 36 93
SEQADV 2ZVX GLY A 14 UNP P00974 CYS 49 ENGINEERED SEQADV 2ZVX ALA A 30 UNP P00974 CYS 65 ENGINEERED SEQADV 2ZVX VAL A 38 UNP P00974 CYS 73 ENGINEERED SEQADV 2ZVX ALA A 51 UNP P00974 CYS 86 ENGINEERED SEQADV 2ZVX LEU A 52 UNP P00974 MET 87 ENGINEERED SEQADV 2ZVX GLY B 14 UNP P00974 CYS 49 ENGINEERED SEQADV 2ZVX ALA B 30 UNP P00974 CYS 65 ENGINEERED SEQADV 2ZVX VAL B 38 UNP P00974 CYS 73 ENGINEERED SEQADV 2ZVX ALA B 51 UNP P00974 CYS 86 ENGINEERED SEQADV 2ZVX LEU B 52 UNP P00974 MET 87 ENGINEERED
SEQRES 1 A 58 ARG PRO ASP PHE CYS LEU GLU PRO PRO TYR THR GLY PRO SEQRES 2 A 58 GLY LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA LYS SEQRES 3 A 58 ALA GLY LEU ALA GLN THR PHE VAL TYR GLY GLY VAL ARG SEQRES 4 A 58 ALA LYS ARG ASN ASN PHE LYS SER ALA GLU ASP ALA LEU SEQRES 5 A 58 ARG THR CYS GLY GLY ALA SEQRES 1 B 58 ARG PRO ASP PHE CYS LEU GLU PRO PRO TYR THR GLY PRO SEQRES 2 B 58 GLY LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA LYS SEQRES 3 B 58 ALA GLY LEU ALA GLN THR PHE VAL TYR GLY GLY VAL ARG SEQRES 4 B 58 ALA LYS ARG ASN ASN PHE LYS SER ALA GLU ASP ALA LEU SEQRES 5 B 58 ARG THR CYS GLY GLY ALA
HET SO4 A4001 5 HET SO4 A4002 5 HET SO4 B4003 5
HETNAM SO4 SULFATE ION
FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *126(H2 O)
HELIX 1 1 SER A 47 GLY A 56 1 10 HELIX 2 2 PRO B 2 GLU B 7 5 6 HELIX 3 3 SER B 47 GLY B 56 1 10
SHEET 1 A 2 ILE A 18 ASN A 24 0 SHEET 2 A 2 LEU 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 LEU B 29 TYR B 35 -1 O TYR B 35 N ILE B 18
SSBOND 1 CYS A 5 CYS A 55 1555 1555 2.06 SSBOND 2 CYS B 5 CYS B 55 1555 1555 2.05
SITE 1 AC1 9 PHE A 4 LYS A 41 ARG A 42 ARG A 53 SITE 2 AC1 9 HOH A 66 HOH A 76 HOH A 98 HOH A 101 SITE 3 AC1 9 ARG B 39 SITE 1 AC2 7 ARG A 20 TYR A 35 GLY A 37 ALA A 40 SITE 2 AC2 7 HOH A 130 HOH A 137 ARG B 42 SITE 1 AC3 8 ARG A 42 HOH A 133 ARG B 20 TYR B 35 SITE 2 AC3 8 ALA B 40 HOH B 89 HOH B 97 HOH B 113
CRYST1 24.962 40.844 54.829 90.00 100.55 90.00 P 1 21 1 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 0.040061 0.000000 0.007461 0.00000
SCALE2 0.000000 0.024483 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018552 0.00000