HEADER HYDROLASE 19-NOV-13 4NOJ TITLE CRYSTAL STRUCTURE OF THE MATURE FORM OF ASPARAGINYL ENDOPEPTIDASE TITLE 2 (AEP)/LEGUMAIN ACTIVATED AT PH 3.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEGUMAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MATURE PROTEIN; COMPND 5 SYNONYM: ASPARAGINYL ENDOPEPTIDASE, PROTEASE, CYSTEINE 1; COMPND 6 EC: 3.4.22.34; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: LGMN, PRSC1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC 1 KEYWDS NEW FOLD, ASPARAGINYL ENDOPEPTIDASE, SUBSTRATE, EXTRACELLULAR, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHAO,T.HUA,H.RU,X.NI,N.SHAW,L.JIAO,W.DING,L.QU,S.OUYANG,Z.J.LIU REVDAT 3 28-FEB-24 4NOJ 1 REMARK REVDAT 2 19-MAR-14 4NOJ 1 JRNL REVDAT 1 19-FEB-14 4NOJ 0 JRNL AUTH L.ZHAO,T.HUA,C.CROWLEY,H.RU,X.NI,N.SHAW,L.JIAO,W.DING,L.QU, JRNL AUTH 2 L.W.HUNG,W.HUANG,L.LIU,K.YE,S.OUYANG,G.CHENG,Z.J.LIU JRNL TITL STRUCTURAL ANALYSIS OF ASPARAGINYL ENDOPEPTIDASE REVEALS THE JRNL TITL 2 ACTIVATION MECHANISM AND A REVERSIBLE INTERMEDIATE JRNL TITL 3 MATURATION STAGE. JRNL REF CELL RES. V. 24 344 2014 JRNL REFN ISSN 1001-0602 JRNL PMID 24407422 JRNL DOI 10.1038/CR.2014.4 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 8038 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 REMARK 3 FREE R VALUE TEST SET COUNT : 371 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.9955 - 4.0371 0.97 2637 140 0.2170 0.2620 REMARK 3 2 4.0371 - 3.2046 0.98 2552 125 0.2217 0.2930 REMARK 3 3 3.2046 - 2.7996 0.96 2478 106 0.2980 0.4233 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 33.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.480 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) : 16.62300 REMARK 3 B22 (A**2) : -12.18680 REMARK 3 B33 (A**2) : -4.43630 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2142 REMARK 3 ANGLE : 0.992 2903 REMARK 3 CHIRALITY : 0.066 304 REMARK 3 PLANARITY : 0.005 376 REMARK 3 DIHEDRAL : 16.244 779 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8038 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M ZINC SULFATE, 0.1 M MES, PH REMARK 280 6.7, AND 23% PEG 500, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 27.65400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.26250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.78950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.26250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.65400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.78950 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 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 ASP A 27 REMARK 465 GLY A 28 REMARK 465 GLY A 29 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 306 O HOH A 320 2.08 REMARK 500 NH2 ARG A 140 O HOH A 321 2.13 REMARK 500 N LYS A 30 O HOH A 304 2.18 REMARK 500 O GLU A 192 OG SER A 195 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 162 NE2 HIS A 254 3654 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 76 -57.00 -121.32 REMARK 500 THR A 84 87.01 -158.84 REMARK 500 PRO A 85 123.59 -38.28 REMARK 500 LYS A 103 49.21 -145.18 REMARK 500 GLU A 108 10.51 -62.25 REMARK 500 LYS A 136 46.52 -108.54 REMARK 500 ASP A 149 -149.61 -171.46 REMARK 500 THR A 153 109.03 -59.81 REMARK 500 ILE A 204 -6.79 -144.94 REMARK 500 PRO A 214 10.53 -61.08 REMARK 500 TYR A 222 73.35 59.62 REMARK 500 VAL A 245 -22.17 -145.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NOK RELATED DB: PDB REMARK 900 RELATED ID: 4NOL RELATED DB: PDB REMARK 900 RELATED ID: 4NOM RELATED DB: PDB DBREF 4NOJ A 27 289 UNP O89017 LGMN_MOUSE 27 289 SEQRES 1 A 263 ASP GLY GLY LYS HIS TRP VAL VAL ILE VAL ALA GLY SER SEQRES 2 A 263 ASN GLY TRP TYR ASN TYR ARG HIS GLN ALA ASP ALA CYS SEQRES 3 A 263 HIS ALA TYR GLN ILE ILE HIS ARG ASN GLY ILE PRO ASP SEQRES 4 A 263 GLU GLN ILE ILE VAL MET MET TYR ASP ASP ILE ALA ASN SEQRES 5 A 263 SER GLU GLU ASN PRO THR PRO GLY VAL VAL ILE ASN ARG SEQRES 6 A 263 PRO ASN GLY THR ASP VAL TYR LYS GLY VAL LEU LYS ASP SEQRES 7 A 263 TYR THR GLY GLU ASP VAL THR PRO GLU ASN PHE LEU ALA SEQRES 8 A 263 VAL LEU ARG GLY ASP ALA GLU ALA VAL LYS GLY LYS GLY SEQRES 9 A 263 SER GLY LYS VAL LEU LYS SER GLY PRO ARG ASP HIS VAL SEQRES 10 A 263 PHE ILE TYR PHE THR ASP HIS GLY ALA THR GLY ILE LEU SEQRES 11 A 263 VAL PHE PRO ASN ASP ASP LEU HIS VAL LYS ASP LEU ASN SEQRES 12 A 263 LYS THR ILE ARG TYR MET TYR GLU HIS LYS MET TYR GLN SEQRES 13 A 263 LYS MET VAL PHE TYR ILE GLU ALA CYS GLU SER GLY SER SEQRES 14 A 263 MET MET ASN HIS LEU PRO ASP ASP ILE ASN VAL TYR ALA SEQRES 15 A 263 THR THR ALA ALA ASN PRO LYS GLU SER SER TYR ALA CYS SEQRES 16 A 263 TYR TYR ASP GLU GLU ARG GLY THR TYR LEU GLY ASP TRP SEQRES 17 A 263 TYR SER VAL ASN TRP MET GLU ASP SER ASP VAL GLU ASP SEQRES 18 A 263 LEU THR LYS GLU THR LEU HIS LYS GLN TYR HIS LEU VAL SEQRES 19 A 263 LYS SER HIS THR ASN THR SER HIS VAL MET GLN TYR GLY SEQRES 20 A 263 ASN LYS SER ILE SER THR MET LYS VAL MET GLN PHE GLN SEQRES 21 A 263 GLY MET LYS FORMUL 2 HOH *23(H2 O) HELIX 1 1 GLY A 41 TYR A 43 5 3 HELIX 2 2 ASN A 44 ASN A 61 1 18 HELIX 3 3 PRO A 64 GLU A 66 5 3 HELIX 4 4 THR A 106 VAL A 110 5 5 HELIX 5 5 THR A 111 GLY A 121 1 11 HELIX 6 6 VAL A 165 HIS A 178 1 14 HELIX 7 7 GLU A 192 MET A 197 5 6 HELIX 8 8 TRP A 234 ASP A 244 1 11 HELIX 9 9 THR A 252 HIS A 263 1 12 HELIX 10 10 LYS A 275 LYS A 281 5 7 HELIX 11 11 VAL A 282 GLY A 287 1 6 SHEET 1 A 6 ILE A 68 MET A 71 0 SHEET 2 A 6 HIS A 31 ALA A 37 1 N ALA A 37 O MET A 71 SHEET 3 A 6 HIS A 142 THR A 148 1 O HIS A 142 N TRP A 32 SHEET 4 A 6 LYS A 183 GLU A 189 1 O GLU A 189 N PHE A 147 SHEET 5 A 6 VAL A 206 THR A 210 1 O THR A 209 N PHE A 186 SHEET 6 A 6 MET A 270 GLY A 273 -1 O TYR A 272 N ALA A 208 SHEET 1 B 3 GLY A 151 ALA A 152 0 SHEET 2 B 3 ILE A 155 VAL A 157 -1 O ILE A 155 N ALA A 152 SHEET 3 B 3 ASP A 162 HIS A 164 -1 O LEU A 163 N LEU A 156 SHEET 1 C 2 ALA A 220 TYR A 223 0 SHEET 2 C 2 TYR A 230 ASP A 233 -1 O GLY A 232 N CYS A 221 CRYST1 55.308 59.579 96.525 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 0.018081 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010360 0.00000