10 20 30 40 50 60 70 80 1CJL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 24-JUL-96 1CJL
TITLE CRYSTAL STRUCTURE OF A CYSTEINE PROTEASE PROFORM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROCATHEPSIN L; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.15; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HUMAN CDNA; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPIC9; SOURCE 9 EXPRESSION_SYSTEM_GENE: HUMAN CDNA; SOURCE 10 OTHER_DETAILS: FIRST RESIDUE (THR) CHANGED TO SER
KEYWDS PROPEPTIDE, INHIBITOR, CYSTEINE PROTEASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.COULOMBE,P.GROCHULSKI,J.SIVARAMAN,M.CYGLER
REVDAT 2 24-FEB-09 1CJL 1 VERSN REVDAT 1 12-AUG-97 1CJL 0
JRNL AUTH R.COULOMBE,P.GROCHULSKI,J.SIVARAMAN,R.MENARD, JRNL AUTH 2 J.S.MORT,M.CYGLER JRNL TITL STRUCTURE OF HUMAN PROCATHEPSIN L REVEALS THE JRNL TITL 2 MOLECULAR BASIS OF INHIBITION BY THE PROSEGMENT. JRNL REF EMBO J. V. 15 5492 1996 JRNL REFN ISSN 0261-4189 JRNL PMID 8896443
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.COULOMBE,Y.LI,S.TAKEBE,R.MENARD,P.MASON,J.S.MORT, REMARK 1 AUTH 2 M.CYGLER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 STUDIES OF HUMAN PROCATHEPSIN L REMARK 1 REF PROTEINS V. 25 398 1996 REMARK 1 REFN ISSN 0887-3585
REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 75.9 REMARK 3 NUMBER OF REFLECTIONS : 13129 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) : 0.182 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1332 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 944 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 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 : 2445 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.18 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL 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) : 2.000 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.000 ; 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 1CJL 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 : 14-MAR-95 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.8 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-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13872 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: ACTINIDIN (PDB ENTRY 1AEC) REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M (NA,K)PO4, PH 7.8
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 20.04000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.46500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.46500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.04000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.04500 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 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 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 THR A 175 REMARK 465 GLU A 176 REMARK 465 SER A 177 REMARK 465 ASP A 178 REMARK 465 GLY A 179
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 14P CD CE NZ REMARK 480 LYS A 37P CG CD CE NZ REMARK 480 LYS A 40P CE NZ REMARK 480 LYS A 53P NZ REMARK 480 ASN A 80P OD1 ND2 REMARK 480 LYS A 85P CG CD CE NZ REMARK 480 LYS A 87P CD CE NZ REMARK 480 ARG A 44 NE CZ NH1 NH2 REMARK 480 LYS A 103 CE NZ REMARK 480 LYS A 120 CG CD CE NZ REMARK 480 ASP A 160 CG OD1 OD2 REMARK 480 ARG A 206 CZ NH1 NH2
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 ASN A 76P -137.37 -101.53 REMARK 500 GLN A 78 -72.94 -59.23 REMARK 500 ALA A 107 66.48 60.04 REMARK 500 LYS A 117 45.45 -74.82 REMARK 500 ALA A 214 58.06 -152.95 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD (CYS 25 IS MUTATED TO SER).
REMARK 999 REMARK 999 SEQUENCE REMARK 999 REMARK 999 PROREGION IS NUMBERED FROM 5P TO 96P WITH "P" IN THE REMARK 999 RESIDUE INSERTION FIELD (COLUMN #17).
DBREF 1CJL A 5P 220 UNP P07711 CATL_HUMAN 22 333
SEQADV 1CJL LEU A 78P UNP P07711 PHE 95 ENGINEERED SEQADV 1CJL SER A 25 UNP P07711 CYS 138 ENGINEERED SEQADV 1CJL GLU A 60 UNP P07711 GLN 173 ENGINEERED SEQADV 1CJL ALA A 110 UNP P07711 THR 223 ENGINEERED SEQADV 1CJL GLY A 179 UNP P07711 ASN 292 CONFLICT
SEQRES 1 A 312 ASP HIS SER LEU GLU ALA GLN TRP THR LYS TRP LYS ALA SEQRES 2 A 312 MET HIS ASN ARG LEU TYR GLY MET ASN GLU GLU GLY TRP SEQRES 3 A 312 ARG ARG ALA VAL TRP GLU LYS ASN MET LYS MET ILE GLU SEQRES 4 A 312 LEU HIS ASN GLN GLU TYR ARG GLU GLY LYS HIS SER PHE SEQRES 5 A 312 THR MET ALA MET ASN ALA PHE GLY ASP MET THR SER GLU SEQRES 6 A 312 GLU PHE ARG GLN VAL MET ASN GLY LEU GLN ASN ARG LYS SEQRES 7 A 312 PRO ARG LYS GLY LYS VAL PHE GLN GLU PRO LEU PHE TYR SEQRES 8 A 312 GLU ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR SEQRES 9 A 312 VAL THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER SER SEQRES 10 A 312 TRP ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET SEQRES 11 A 312 PHE ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN SEQRES 12 A 312 ASN LEU VAL ASP CYS SER GLY PRO GLU GLY ASN GLU GLY SEQRES 13 A 312 CYS ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL SEQRES 14 A 312 GLN ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO SEQRES 15 A 312 TYR GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS SEQRES 16 A 312 TYR SER VAL ALA ASN ASP ALA GLY PHE VAL ASP ILE PRO SEQRES 17 A 312 LYS GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL SEQRES 18 A 312 GLY PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER SEQRES 19 A 312 PHE LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP SEQRES 20 A 312 CYS SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL SEQRES 21 A 312 GLY TYR GLY PHE GLU SER THR GLU SER ASP GLY ASN LYS SEQRES 22 A 312 TYR TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY SEQRES 23 A 312 MET GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN SEQRES 24 A 312 HIS CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL
FORMUL 2 HOH *71(H2 O)
HELIX 1 1 HIS A 6P MET A 18P 1 13 HELIX 2 2 MET A 25P ARG A 50P 1 26 HELIX 3 3 SER A 68P VAL A 74P 1 7 HELIX 4 4 TRP A 7 GLU A 9 5 3 HELIX 5 5 SER A 25 THR A 42 1 18 HELIX 6 6 GLU A 50 GLU A 60 1 11 HELIX 7 7 GLY A 64 ASN A 66 5 3 HELIX 8 8 MET A 70 ASN A 80 1 11 HELIX 9 9 PRO A 102 TYR A 104 5 3 HELIX 10 10 GLU A 119 VAL A 129 1 11 HELIX 11 11 GLU A 141 LEU A 144 1 4 HELIX 12 12 HIS A 208 GLY A 210 5 3
SHEET 1 A 2 GLY A 111 ASP A 114 0 SHEET 2 A 2 SER A 216 THR A 219 -1 N THR A 219 O GLY A 111 SHEET 1 B 4 ILE A 132 ILE A 136 0 SHEET 2 B 4 HIS A 163 PHE A 172 -1 N VAL A 167 O ILE A 132 SHEET 3 B 4 LYS A 181 LYS A 186 -1 N LYS A 186 O LEU A 166 SHEET 4 B 4 TYR A 198 ALA A 202 -1 N MET A 201 O TRP A 183 SHEET 1 C 2 PHE A 56P MET A 58P 0 SHEET 2 C 2 TYR A 146 GLY A 149 -1 N GLU A 148 O THR A 57P
SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.02 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.04 SSBOND 3 CYS A 156 CYS A 209 1555 1555 2.03
SITE 1 ACT 3 SER A 25 HIS A 163 ASN A 187
CRYST1 40.080 88.090 94.930 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 0.024950 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011352 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010534 0.00000