HEADER SERINE PROTEASE 24-JUL-96 1AKS
TITLE CRYSTAL STRUCTURE OF THE FIRST ACTIVE AUTOLYSATE FORM OF
TITLE 2 THE PORCINE ALPHA TRYPSIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA TRYPSIN;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.4.21.4;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: ALPHA TRYPSIN;
COMPND 7 CHAIN: B;
COMPND 8 EC: 3.4.21.4
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA;
SOURCE 3 ORGANISM_COMMON: PIG;
SOURCE 4 ORGANISM_TAXID: 9823;
SOURCE 5 ORGAN: PANCREAS;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: SUS SCROFA;
SOURCE 8 ORGANISM_COMMON: PIG;
SOURCE 9 ORGANISM_TAXID: 9823;
SOURCE 10 ORGAN: PANCREAS
KEYWDS HYDROLASE, SERINE PROTEASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.JOHNSON,S.KRISHNASWAMY,P.V.SUNDARAM,V.PATTABHI
REVDAT 2 24-FEB-09 1AKS 1 VERSN
REVDAT 1 12-FEB-97 1AKS 0
JRNL AUTH A.JOHNSON,S.KRISHNASWAMY,P.V.SUNDARAM,V.PATTABHI
JRNL TITL THE FIRST STRUCTURE AT 1.8 A RESOLUTION OF AN
JRNL TITL 2 ACTIVE AUTOLYSATE FORM OF PORCINE ALPHA-TRYSOIN.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 53 311 1997
JRNL REFN ISSN 0907-4449
JRNL PMID 15299934
JRNL DOI 10.1107/S0907444997000358
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 17698
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.200
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2032
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 111
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.011
REMARK 3 BOND ANGLES (DEGREES) : 1.68
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.85
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1AKS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
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) : NULL
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: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.23
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 38.85000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.54000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.91000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.54000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.85000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.91000
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5640 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 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 HIS A 71 -64.23 -126.12
REMARK 500 SER B 150 97.76 168.11
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 146 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 70 OE1
REMARK 620 2 ASN A 72 O 87.9
REMARK 620 3 VAL A 75 O 143.2 87.6
REMARK 620 4 GLU A 77 OE2 100.5 108.7 115.5
REMARK 620 5 GLU A 80 OE2 94.0 175.0 88.1 75.5
REMARK 620 6 HOH A 197 O 74.0 92.9 69.8 157.6 83.2
REMARK 620 N 1 2 3 4 5
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 146
REMARK 999
REMARK 999 SEQUENCE
REMARK 999
REMARK 999 THE 223 AMINO ACIDS OF TRYPSIN ARE IDENTIFIED BY THE
REMARK 999 RESIDUE NUMBERS OF THE HOMOLOGOUS CHYMOTRYPSINOGEN.
REMARK 999 IN THIS ENTRY TWO CHAINS OF TRYPSIN ARE GIVEN IDENTIFIERS
REMARK 999 "A" (RESIDUES 16 - 145) AND "B" (RESIDUES 146 - 245).
DBREF 1AKS A 16 145 UNP P00761 TRYP_PIG 9 133
DBREF 1AKS B 146 245 UNP P00761 TRYP_PIG 134 231
SEQADV 1AKS ASN B 165 UNP P00761 ASP 153 CONFLICT
SEQADV 1AKS GLN B 186 UNP P00761 GLU 175 CONFLICT
SEQRES 1 A 125 ILE VAL GLY GLY TYR THR CYS ALA ALA ASN SER ILE PRO
SEQRES 2 A 125 TYR GLN VAL SER LEU ASN SER GLY SER HIS PHE CYS GLY
SEQRES 3 A 125 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA
SEQRES 4 A 125 HIS CYS TYR LYS SER ARG ILE GLN VAL ARG LEU GLY GLU
SEQRES 5 A 125 HIS ASN ILE ASP VAL LEU GLU GLY ASN GLU GLN PHE ILE
SEQRES 6 A 125 ASN ALA ALA LYS ILE ILE THR HIS PRO ASN PHE ASN GLY
SEQRES 7 A 125 ASN THR LEU ASP ASN ASP ILE MET LEU ILE LYS LEU SER
SEQRES 8 A 125 SER PRO ALA THR LEU ASN SER ARG VAL ALA THR VAL SER
SEQRES 9 A 125 LEU PRO ARG SER CYS ALA ALA ALA GLY THR GLU CYS LEU
SEQRES 10 A 125 ILE SER GLY TRP GLY ASN THR LYS
SEQRES 1 B 98 SER SER GLY SER SER TYR PRO SER LEU LEU GLN CYS LEU
SEQRES 2 B 98 LYS ALA PRO VAL LEU SER ASN SER SER CYS LYS SER SER
SEQRES 3 B 98 TYR PRO GLY GLN ILE THR GLY ASN MET ILE CYS VAL GLY
SEQRES 4 B 98 PHE LEU GLN GLY GLY LYS ASP SER CYS GLN GLY ASP SER
SEQRES 5 B 98 GLY GLY PRO VAL VAL CYS ASN GLY GLN LEU GLN GLY ILE
SEQRES 6 B 98 VAL SER TRP GLY TYR GLY CYS ALA GLN LYS ASN LYS PRO
SEQRES 7 B 98 GLY VAL TYR THR LYS VAL CYS ASN TYR VAL ASN TRP ILE
SEQRES 8 B 98 GLN GLN THR ILE ALA ALA ASN
HET CA A 146 1
HETNAM CA CALCIUM ION
FORMUL 3 CA CA 2+
FORMUL 4 HOH *111(H2 O)
HELIX 1 H1 ALA A 56 CYS A 58 5 3
HELIX 2 H2 ASN B 165 SER B 171 1 7
HELIX 3 H3 VAL B 231 ASN B 233 5 3
HELIX 4 H4 VAL B 235 ALA B 244 1 10
SHEET 1 A 4 GLN A 81 ASN A 84 0
SHEET 2 A 4 GLN A 64 LEU A 67 -1 N LEU A 67 O GLN A 81
SHEET 3 A 4 GLN A 30 ASN A 34 -1 N ASN A 34 O GLN A 64
SHEET 4 A 4 HIS A 40 SER A 45 -1 N GLY A 44 O VAL A 31
SHEET 1 B 3 TRP A 51 SER A 54 0
SHEET 2 B 3 MET A 104 LEU A 108 -1 N ILE A 106 O VAL A 52
SHEET 3 B 3 ALA A 85 THR A 90 -1 N ILE A 89 O LEU A 105
SHEET 1 C 2 GLU A 135 GLY A 140 0
SHEET 2 C 2 GLN B 156 PRO B 161 -1 N ALA B 160 O CYS A 136
SHEET 1 D 4 MET B 180 VAL B 183 0
SHEET 2 D 4 GLY B 226 LYS B 230 -1 N TYR B 228 O ILE B 181
SHEET 3 D 4 GLN B 204 TRP B 215 -1 N TRP B 215 O VAL B 227
SHEET 4 D 4 PRO B 198 CYS B 201 -1 N CYS B 201 O GLN B 204
SSBOND 1 CYS A 22 CYS B 157 1555 1555 2.05
SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.05
SSBOND 3 CYS A 128 CYS B 232 1555 1555 2.04
SSBOND 4 CYS A 136 CYS B 201 1555 1555 2.04
SSBOND 5 CYS B 168 CYS B 182 1555 1555 2.04
SSBOND 6 CYS B 191 CYS B 220 1555 1555 2.05
LINK CA CA A 146 OE1 GLU A 70 1555 1555 2.34
LINK CA CA A 146 O ASN A 72 1555 1555 2.11
LINK CA CA A 146 O VAL A 75 1555 1555 2.26
LINK CA CA A 146 OE2 GLU A 77 1555 1555 1.89
LINK CA CA A 146 OE2 GLU A 80 1555 1555 2.50
LINK CA CA A 146 O HOH A 197 1555 1555 1.58
SITE 1 AC1 6 GLU A 70 ASN A 72 VAL A 75 GLU A 77
SITE 2 AC1 6 GLU A 80 HOH A 197
CRYST1 77.700 53.820 47.080 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 0.012870 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018580 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021240 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
