HEADER HYDROLASE 09-NOV-08 3F7M TITLE CRYSTAL STRUCTURE OF APO CUTICLE-DEGRADING PROTEASE (VER112) FROM TITLE 2 VERTICILLIUM PSALLIOTAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKALINE SERINE PROTEASE VER112; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LECANICILLIUM PSALLIOTAE; SOURCE 3 ORGANISM_TAXID: 73499 KEYWDS VERTICILLIUM PSALLIOTAE, CUTICLE-DEGRADING PROTEASE, NEMATODES, KEYWDS 2 HYDROLASE, PROTEASE, SECRETED, SERINE PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR L.LIANG,Z.LOU,F.YE,Z.MENG,Z.RAO,K.ZHANG REVDAT 4 30-OCT-24 3F7M 1 REMARK REVDAT 3 01-NOV-23 3F7M 1 SEQADV REVDAT 2 02-APR-14 3F7M 1 JRNL VERSN SOURCE REVDAT 1 17-NOV-09 3F7M 0 JRNL AUTH L.LIANG,Z.MENG,F.YE,J.YANG,S.LIU,Y.SUN,Y.GUO,Q.MI,X.HUANG, JRNL AUTH 2 C.ZOU,Z.RAO,Z.LOU,K.Q.ZHANG JRNL TITL THE CRYSTAL STRUCTURES OF TWO CUTICLE-DEGRADING PROTEASES JRNL TITL 2 FROM NEMATOPHAGOUS FUNGI AND THEIR CONTRIBUTION TO INFECTION JRNL TITL 3 AGAINST NEMATODES. JRNL REF FASEB J. V. 24 1391 2010 JRNL REFN ISSN 0892-6638 JRNL PMID 20007510 JRNL DOI 10.1096/FJ.09-136408 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.7 REMARK 3 NUMBER OF REFLECTIONS : 22871 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1107 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 : 2004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 247 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) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.266 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 3F7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRROR REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26891 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.03400 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.13800 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1BJR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K 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 21.84000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.17350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.91550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.17350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.91550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 ASP A 143 -141.32 -162.69 REMARK 500 ASP A 148 0.59 -67.57 REMARK 500 ARG A 230 175.78 139.95 REMARK 500 TYR A 299 -158.89 -145.28 REMARK 500 ARG A 320 -164.48 -100.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F7O RELATED DB: PDB DBREF 3F7M A 104 382 UNP Q68GV9 ALP_LECPS 104 382 SEQADV 3F7M ILE A 212 UNP Q68GV9 VAL 212 CONFLICT SEQRES 1 A 279 ILE THR GLN GLN GLN GLY ALA THR TRP GLY LEU THR ARG SEQRES 2 A 279 ILE SER HIS ARG ALA ARG GLY SER THR ALA TYR ALA TYR SEQRES 3 A 279 ASP THR SER ALA GLY ALA GLY ALA CYS VAL TYR VAL ILE SEQRES 4 A 279 ASP THR GLY VAL GLU ASP THR HIS PRO ASP PHE GLU GLY SEQRES 5 A 279 ARG ALA LYS GLN ILE LYS SER TYR ALA SER THR ALA ARG SEQRES 6 A 279 ASP GLY HIS GLY HIS GLY THR HIS CYS ALA GLY THR ILE SEQRES 7 A 279 GLY SER LYS THR TRP GLY VAL ALA LYS LYS VAL SER ILE SEQRES 8 A 279 PHE GLY VAL LYS VAL LEU ASP ASP SER GLY SER GLY SER SEQRES 9 A 279 LEU SER ASN ILE ILE ALA GLY MET ASP PHE VAL ALA SER SEQRES 10 A 279 ASP ARG GLN SER ARG ASN CYS PRO ARG ARG THR VAL ALA SEQRES 11 A 279 SER MET SER LEU GLY GLY GLY TYR SER ALA ALA LEU ASN SEQRES 12 A 279 GLN ALA ALA ALA ARG LEU GLN SER SER GLY VAL PHE VAL SEQRES 13 A 279 ALA VAL ALA ALA GLY ASN ASP ASN ARG ASP ALA ALA ASN SEQRES 14 A 279 THR SER PRO ALA SER GLU PRO THR VAL CYS THR VAL GLY SEQRES 15 A 279 ALA THR ASP SER ASN ASP VAL ARG SER THR PHE SER ASN SEQRES 16 A 279 TYR GLY ARG VAL VAL ASP ILE PHE ALA PRO GLY THR SER SEQRES 17 A 279 ILE THR SER THR TRP ILE GLY GLY ARG THR ASN THR ILE SEQRES 18 A 279 SER GLY THR SER MET ALA THR PRO HIS ILE ALA GLY LEU SEQRES 19 A 279 ALA ALA TYR LEU PHE GLY LEU GLU GLY GLY SER ALA GLY SEQRES 20 A 279 ALA MET CYS GLY ARG ILE GLN THR LEU SER THR LYS ASN SEQRES 21 A 279 VAL LEU THR SER ILE PRO SER GLY THR VAL ASN TYR LEU SEQRES 22 A 279 ALA PHE ASN GLY ALA THR FORMUL 2 HOH *247(H2 O) HELIX 1 1 THR A 111 SER A 118 1 8 HELIX 2 2 HIS A 150 GLU A 154 5 5 HELIX 3 3 GLY A 172 SER A 183 1 12 HELIX 4 4 SER A 207 ARG A 222 1 16 HELIX 5 5 GLN A 223 ARG A 225 5 3 HELIX 6 6 SER A 242 SER A 255 1 14 HELIX 7 7 ASP A 269 ALA A 271 5 3 HELIX 8 8 ILE A 317 GLY A 319 5 3 HELIX 9 9 GLY A 326 GLU A 345 1 20 HELIX 10 10 ALA A 351 SER A 360 1 10 SHEET 1 A 2 THR A 105 GLN A 107 0 SHEET 2 A 2 TYR A 127 TYR A 129 -1 O TYR A 129 N THR A 105 SHEET 1 B 7 ALA A 157 SER A 162 0 SHEET 2 B 7 SER A 193 LYS A 198 1 O LYS A 198 N LYS A 161 SHEET 3 B 7 ALA A 137 ASP A 143 1 N VAL A 141 O PHE A 195 SHEET 4 B 7 ARG A 230 MET A 235 1 O SER A 234 N TYR A 140 SHEET 5 B 7 PHE A 258 ALA A 262 1 O ALA A 260 N MET A 235 SHEET 6 B 7 CYS A 282 THR A 287 1 O VAL A 284 N VAL A 261 SHEET 7 B 7 ILE A 305 PRO A 308 1 O ILE A 305 N GLY A 285 SHEET 1 C 2 GLY A 239 GLY A 240 0 SHEET 2 C 2 THR A 273 SER A 274 -1 O SER A 274 N GLY A 239 SHEET 1 D 2 ILE A 312 THR A 315 0 SHEET 2 D 2 THR A 321 ILE A 324 -1 O ILE A 324 N ILE A 312 SHEET 1 E 2 THR A 361 LYS A 362 0 SHEET 2 E 2 TYR A 375 LEU A 376 -1 O LEU A 376 N THR A 361 SSBOND 1 CYS A 138 CYS A 227 1555 1555 2.03 SSBOND 2 CYS A 282 CYS A 353 1555 1555 2.04 CISPEP 1 SER A 274 PRO A 275 0 0.27 CRYST1 43.680 67.831 76.347 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 0.022894 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013098 0.00000