HEADER PROTEIN TRANSPORT 06-JAN-23 8HYG TITLE CRYSTAL STRUCTURE OF PROTEASE-ASSOCIATED DOMAIN OF ARABIDOPSIS TITLE 2 VACUOLAR SORTING RECEPTOR 1 AT PH 4.6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR-SORTING RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEASE ASSOCIATED DOMAIN; COMPND 5 SYNONYM: ATVSR1,BP80-LIKE PROTEIN B,ATBP80B,EPIDERMAL GROWTH FACTOR COMPND 6 RECEPTOR-LIKE PROTEIN 1,ATELP,ATELP1,SPOT 3 PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: VSR1, BP80B, ELP, ELP1, AT3G52850, F8J2.20; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VSR, VACUOLAR SORTING, PROTEASE-ASSOCIATED DOMAIN, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.E.TSAO,S.N.LUI,K.B.WONG REVDAT 1 25-JAN-23 8HYG 0 JRNL AUTH H.E.TSAO,S.N.LUI,K.B.WONG JRNL TITL CRYSTAL STRUCTURE OF PROTEASE-ASSOCIATED DOMAIN OF JRNL TITL 2 ARABIDOPSIS VACUOLAR SORTING RECEPTOR 1 AT PH 4.6 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 941 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 31.8000 - 3.0600 0.97 2624 119 0.1577 0.1955 REMARK 3 2 3.0600 - 2.4300 1.00 2630 139 0.1828 0.2373 REMARK 3 3 2.4300 - 2.1200 1.00 2621 153 0.1729 0.2644 REMARK 3 4 2.1200 - 1.9300 1.00 2610 142 0.1581 0.2006 REMARK 3 5 1.9300 - 1.7900 1.00 2641 121 0.1670 0.2349 REMARK 3 6 1.7900 - 1.6800 1.00 2632 136 0.1910 0.2718 REMARK 3 7 1.6800 - 1.6000 1.00 2598 131 0.2358 0.3040 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) : 0.184 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.439 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.26 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 : 0.005 1167 REMARK 3 ANGLE : 0.695 1580 REMARK 3 CHIRALITY : 0.053 189 REMARK 3 PLANARITY : 0.004 197 REMARK 3 DIHEDRAL : 12.710 424 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 8HYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 37.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 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: PHASER REMARK 200 STARTING MODEL: 4TJV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6, 30% W/V POLYETHYLENE GLYCOL 4,000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.15900 REMARK 290 SMTRY3 2 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 VAL A 49 REMARK 465 PRO A 50 REMARK 465 GLN A 51 REMARK 465 TYR A 52 REMARK 465 GLY A 53 REMARK 465 GLU A 132 REMARK 465 GLU A 133 REMARK 465 ASP A 134 REMARK 465 LYS A 135 REMARK 465 SER A 136 REMARK 465 ASP A 137 REMARK 465 ALA A 138 REMARK 465 GLU A 177 REMARK 465 SER A 178 REMARK 465 VAL A 179 REMARK 465 PRO A 180 REMARK 465 HIS A 181 REMARK 465 PRO A 182 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 LYS A 29 CE NZ REMARK 470 ASP A 34 OD1 OD2 REMARK 470 LYS A 37 CD CE NZ REMARK 470 GLY A 48 C O REMARK 470 GLY A 54 N CA O REMARK 470 LYS A 64 CD CE NZ REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 LYS A 83 CD CE NZ REMARK 470 ARG A 86 CD NE CZ NH1 NH2 REMARK 470 THR A 130 OG1 CG2 REMARK 470 ASP A 139 CG OD1 OD2 REMARK 470 LEU A 141 CD1 CD2 REMARK 470 ASP A 174 CG OD1 OD2 REMARK 470 TRP A 175 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 175 CZ3 CH2 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 97 -27.65 72.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 202 REMARK 610 EPE A 204 REMARK 610 PEG A 205 REMARK 610 PEG A 206 DBREF 8HYG A 20 182 UNP P93026 VSR1_ARATH 20 182 SEQADV 8HYG GLY A 18 UNP P93026 EXPRESSION TAG SEQADV 8HYG SER A 19 UNP P93026 EXPRESSION TAG SEQRES 1 A 165 GLY SER ARG PHE VAL VAL GLU LYS ASN ASN LEU LYS VAL SEQRES 2 A 165 THR SER PRO ASP SER ILE LYS GLY ILE TYR GLU CYS ALA SEQRES 3 A 165 ILE GLY ASN PHE GLY VAL PRO GLN TYR GLY GLY THR LEU SEQRES 4 A 165 VAL GLY THR VAL VAL TYR PRO LYS SER ASN GLN LYS ALA SEQRES 5 A 165 CYS LYS SER TYR SER ASP PHE ASP ILE SER PHE LYS SER SEQRES 6 A 165 LYS PRO GLY ARG LEU PRO THR PHE VAL LEU ILE ASP ARG SEQRES 7 A 165 GLY ASP CYS TYR PHE THR LEU LYS ALA TRP ILE ALA GLN SEQRES 8 A 165 GLN ALA GLY ALA ALA ALA ILE LEU VAL ALA ASP SER LYS SEQRES 9 A 165 ALA GLU PRO LEU ILE THR MET ASP THR PRO GLU GLU ASP SEQRES 10 A 165 LYS SER ASP ALA ASP TYR LEU GLN ASN ILE THR ILE PRO SEQRES 11 A 165 SER ALA LEU ILE THR LYS THR LEU GLY ASP SER ILE LYS SEQRES 12 A 165 SER ALA LEU SER GLY GLY ASP MET VAL ASN MET LYS LEU SEQRES 13 A 165 ASP TRP THR GLU SER VAL PRO HIS PRO HET ACT A 201 4 HET PEG A 202 5 HET CL A 203 1 HET EPE A 204 13 HET PEG A 205 5 HET PEG A 206 5 HET PEG A 207 7 HET ACT A 208 4 HET ACT A 209 4 HET ACT A 210 4 HET PEG A 211 7 HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 ACT 4(C2 H3 O2 1-) FORMUL 3 PEG 5(C4 H10 O3) FORMUL 4 CL CL 1- FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 13 HOH *70(H2 O) HELIX 1 AA1 PRO A 33 LYS A 37 5 5 HELIX 2 AA2 SER A 72 ASP A 77 5 6 HELIX 3 AA3 TYR A 99 ALA A 110 1 12 HELIX 4 AA4 PRO A 124 ASP A 129 1 6 HELIX 5 AA5 TYR A 140 ILE A 144 5 5 HELIX 6 AA6 THR A 152 GLY A 165 1 14 SHEET 1 AA1 8 PHE A 21 SER A 32 0 SHEET 2 AA1 8 GLY A 38 GLY A 45 -1 O CYS A 42 N GLU A 24 SHEET 3 AA1 8 SER A 148 ILE A 151 -1 O SER A 148 N GLY A 45 SHEET 4 AA1 8 ALA A 114 ALA A 118 1 N VAL A 117 O ALA A 149 SHEET 5 AA1 8 THR A 89 ASP A 94 1 N ILE A 93 O LEU A 116 SHEET 6 AA1 8 LEU A 56 VAL A 61 1 N THR A 59 O PHE A 90 SHEET 7 AA1 8 ASN A 170 LEU A 173 -1 O LEU A 173 N LEU A 56 SHEET 8 AA1 8 PHE A 21 SER A 32 -1 N LYS A 29 O LYS A 172 SSBOND 1 CYS A 70 CYS A 98 1555 1555 2.05 CISPEP 1 SER A 32 PRO A 33 0 -1.85 CRYST1 32.987 60.318 38.466 90.00 103.36 90.00 P 1 21 1 2 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 0.030315 0.000000 0.007200 0.00000 SCALE2 0.000000 0.016579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026720 0.00000