HEADER HYDROLASE 03-JUN-26 27JK TITLE CRYSTAL STRUCTURE OF THE MATURE FORM OF HUMAN ASPRV1 (K199E, FORM 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETROVIRAL-LIKE ASPARTIC PROTEASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SKIN-SPECIFIC RETROVIRAL-LIKE ASPARTIC PROTEASE,SASPASE,SKIN COMPND 5 ASPARTIC PROTEASE,TPA-INDUCIBLE ASPARTIC PROTEINASE-LIKE PROTEIN, COMPND 6 TAPS; COMPND 7 EC: 3.4.23.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ASPRV1, SASP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RETROVIRAL-LIKE ASPARTIC PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHEN,X.FENG,J.DING REVDAT 1 02-SEP-26 27JK 0 JRNL AUTH X.FENG,Z.CHEN,C.LAN,J.DING JRNL TITL STRUCTURE AND ENZYMATIC PROPERTIES OF HUMAN RETROVIRAL-LIKE JRNL TITL 2 ASPARTIC PROTEASE 1 AND FUNCTIONAL ROLES OF JRNL TITL 3 DISEASE-ASSOCIATED MUTATIONS. JRNL REF ACTA BIOCHIM.BIOPHYS.SIN. 2026 JRNL REFN ESSN 1745-7270 JRNL PMID 42593882 JRNL DOI 10.3724/ABBS.2026141 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 11141 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.560 REMARK 3 FREE R VALUE TEST SET COUNT : 619 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 24.1500 - 2.9200 1.00 2750 177 0.1912 0.1956 REMARK 3 2 2.9200 - 2.3200 1.00 2643 158 0.2312 0.2787 REMARK 3 3 2.3200 - 2.0300 1.00 2656 134 0.2239 0.2633 REMARK 3 4 2.0200 - 1.8400 0.95 2473 150 0.2301 0.2970 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.16 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 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 : 0.007 1070 REMARK 3 ANGLE : 0.902 1447 REMARK 3 CHIRALITY : 0.063 167 REMARK 3 PLANARITY : 0.006 186 REMARK 3 DIHEDRAL : 15.726 389 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 27JK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 10-JUN-26. REMARK 100 THE DEPOSITION ID IS D_1300075121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-25 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL18U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 24.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CALCIUM CHLORIDE DIHYDRATE, 0.1 REMARK 280 M MES MONOHYDRATE, PH 6.0, AND 45% (V/V) PEG 200, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.26000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.26000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.38500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.26000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.45000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.38500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.26000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.45000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 32.38500 REMARK 290 SMTRY3 8 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: 4860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 38.26000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 511 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 535 LIES ON A SPECIAL POSITION. 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 241 -164.39 -110.38 REMARK 500 THR A 259 -154.88 -148.67 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 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 230 OD2 REMARK 620 2 GLN A 290 O 13.9 REMARK 620 3 ASN A 293 OD1 10.6 3.8 REMARK 620 4 GLU A 299 OE2 27.3 31.5 31.4 REMARK 620 5 HOH A 519 O 91.6 97.1 97.2 65.7 REMARK 620 6 HOH A 532 O 86.9 88.1 86.2 113.8 151.9 REMARK 620 N 1 2 3 4 5 DBREF 27JK A 191 326 UNP Q53RT3 APRV1_HUMAN 191 326 SEQADV 27JK SER A 190 UNP Q53RT3 EXPRESSION TAG SEQADV 27JK GLU A 199 UNP Q53RT3 LYS 199 CONFLICT SEQRES 1 A 137 SER SER MET GLY LYS GLY TYR TYR LEU GLU GLY LYS ILE SEQRES 2 A 137 GLY LYS VAL PRO VAL ARG PHE LEU VAL ASP SER GLY ALA SEQRES 3 A 137 GLN VAL SER VAL VAL HIS PRO ASN LEU TRP GLU GLU VAL SEQRES 4 A 137 THR ASP GLY ASP LEU ASP THR LEU GLN PRO PHE GLU ASN SEQRES 5 A 137 VAL VAL LYS VAL ALA ASN GLY ALA GLU MET LYS ILE LEU SEQRES 6 A 137 GLY VAL TRP ASP THR ALA VAL SER LEU GLY LYS LEU LYS SEQRES 7 A 137 LEU LYS ALA GLN PHE LEU VAL ALA ASN ALA SER ALA GLU SEQRES 8 A 137 GLU ALA ILE ILE GLY THR ASP VAL LEU GLN ASP HIS ASN SEQRES 9 A 137 ALA ILE LEU ASP PHE GLU HIS ARG THR CYS THR LEU LYS SEQRES 10 A 137 GLY LYS LYS PHE ARG LEU LEU PRO VAL GLY GLY SER LEU SEQRES 11 A 137 GLU ASP GLU PHE ASP LEU GLU HET CA A 401 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *40(H2 O) HELIX 1 AA1 HIS A 221 ASP A 230 1 10 HELIX 2 AA2 ASP A 232 LEU A 236 5 5 HELIX 3 AA3 GLY A 285 HIS A 292 1 8 SHEET 1 AA1 8 LEU A 313 VAL A 315 0 SHEET 2 AA1 8 GLY A 195 ILE A 202 -1 N GLY A 195 O VAL A 315 SHEET 3 AA1 8 GLY A 255 LEU A 263 -1 O SER A 262 N LYS A 201 SHEET 4 AA1 8 LEU A 266 VAL A 274 -1 O LEU A 266 N LEU A 263 SHEET 5 AA1 8 SER A 218 VAL A 220 1 N SER A 218 O LEU A 273 SHEET 6 AA1 8 ALA A 282 ILE A 284 -1 O ILE A 283 N VAL A 219 SHEET 7 AA1 8 VAL A 205 VAL A 211 1 N LEU A 210 O ILE A 284 SHEET 8 AA1 8 GLY A 195 ILE A 202 -1 N LEU A 198 O PHE A 209 SHEET 1 AA2 3 ILE A 295 ASP A 297 0 SHEET 2 AA2 3 THR A 302 LEU A 305 -1 O THR A 302 N ASP A 297 SHEET 3 AA2 3 LYS A 308 ARG A 311 -1 O LYS A 308 N LEU A 305 LINK OD2 ASP A 230 CA CA A 401 1555 1555 2.28 LINK O GLN A 290 CA CA A 401 1555 8545 2.66 LINK OD1 ASN A 293 CA CA A 401 1555 8545 2.34 LINK OE2 GLU A 299 CA CA A 401 1555 6445 2.43 LINK CA CA A 401 O HOH A 519 1555 1555 2.52 LINK CA CA A 401 O HOH A 532 1555 8445 2.46 CRYST1 50.900 64.770 76.520 90.00 90.00 90.00 C 2 2 21 8 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 0.019646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013068 0.00000 CONECT 316 1054 CONECT 1054 316 1073 CONECT 1073 1054 MASTER 258 0 1 3 11 0 0 6 1093 1 3 11 END