HEADER PROTEIN TRANSPORT 10-JUN-21 7F2D TITLE ARABIDOPSIS THALIANA PROTEASE-ASSOCIATED DOMAIN OF VACUOLAR-SORTING TITLE 2 RECEPTOR 1 IN COMPLEX WITH CRUCIFERIN 1 C-TERMINAL PENTAPEPTIDE RVAAA TITLE 3 (PH9) 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CRUCIFERIN 1 C-TERMINAL PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 11 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 12 ORGANISM_TAXID: 3702 KEYWDS LIGAND-BINDING DOMAIN RECEPTOR-CARGO INTERACTION CRUCIFERIN PEPTIDE, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.N.LUI,K.B.WONG REVDAT 2 29-NOV-23 7F2D 1 REMARK REVDAT 1 12-JAN-22 7F2D 0 JRNL AUTH H.E.TSAO,S.N.LUI,A.H.LO,S.CHEN,H.Y.WONG,C.K.WONG,L.JIANG, JRNL AUTH 2 K.B.WONG JRNL TITL STRUCTURAL INSIGHTS INTO HOW VACUOLAR SORTING RECEPTORS JRNL TITL 2 RECOGNIZE THE SORTING DETERMINANTS OF SEED STORAGE PROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 34983843 JRNL DOI 10.1073/PNAS.2111281119 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 5286 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 275 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 37.7400 - 4.6900 0.98 742 38 0.1675 0.2431 REMARK 3 2 4.6800 - 3.7200 0.97 741 33 0.1613 0.2240 REMARK 3 3 3.7200 - 3.2500 0.97 716 36 0.1941 0.2361 REMARK 3 4 3.2500 - 2.9500 0.96 711 31 0.2089 0.2047 REMARK 3 5 2.9500 - 2.7400 0.96 692 50 0.2118 0.2527 REMARK 3 6 2.7400 - 2.5800 0.95 726 40 0.2046 0.2549 REMARK 3 7 2.5800 - 2.4500 0.95 683 47 0.1644 0.2654 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.04 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.7777 33.3663 8.1154 REMARK 3 T TENSOR REMARK 3 T11: 0.1022 T22: 0.1264 REMARK 3 T33: 0.1017 T12: -0.0131 REMARK 3 T13: -0.0051 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.9094 L22: 2.5389 REMARK 3 L33: 1.4224 L12: -0.0076 REMARK 3 L13: 0.2216 L23: 0.4027 REMARK 3 S TENSOR REMARK 3 S11: -0.0504 S12: -0.0214 S13: -0.0356 REMARK 3 S21: -0.0020 S22: 0.0490 S23: 0.0466 REMARK 3 S31: 0.0067 S32: 0.0086 S33: 0.0035 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 7F2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 9.0 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5308 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 37.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08600 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: MOLREP REMARK 200 STARTING MODEL: 4TJX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 30% W/V POLYETHYLENE REMARK 280 GLYCOL MONOMETHYL ETHER 2000, PH 9.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 289.15K 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 30.38350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 18 REMARK 465 SER A 19 REMARK 465 ARG A 20 REMARK 465 PHE A 21 REMARK 465 VAL A 22 REMARK 465 VAL A 23 REMARK 465 GLY A 48 REMARK 465 VAL A 49 REMARK 465 PRO A 50 REMARK 465 GLN A 51 REMARK 465 TYR A 52 REMARK 465 LYS A 135 REMARK 465 SER A 136 REMARK 465 ASP A 137 REMARK 465 ALA A 138 REMARK 465 THR A 176 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 GLU A 24 N CB CG CD OE1 OE2 REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 LYS A 81 CD CE NZ REMARK 470 LYS A 83 CE NZ REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 ASP A 134 C O CB CG OD1 OD2 REMARK 470 ASP A 139 N CB CG OD1 OD2 REMARK 470 GLN A 142 CG CD OE1 NE2 REMARK 470 ARG B 1 CG CD NE 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 26 -158.90 -120.41 REMARK 500 ASP A 97 -23.24 76.51 REMARK 500 GLU A 132 -32.68 69.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 7F2D A 20 182 UNP P93026 VSR1_ARATH 20 182 DBREF 7F2D B 1 5 UNP P15455 CRU1_ARATH 468 472 SEQADV 7F2D GLY A 18 UNP P93026 EXPRESSION TAG SEQADV 7F2D 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 SEQRES 1 B 5 ARG VAL ALA ALA ALA FORMUL 3 HOH *65(H2 O) HELIX 1 AA1 SER A 72 PHE A 76 5 5 HELIX 2 AA2 TYR A 99 ALA A 110 1 12 HELIX 3 AA3 ASP A 139 ILE A 144 5 6 HELIX 4 AA4 THR A 152 GLY A 165 1 14 SHEET 1 AA1 8 ASN A 26 SER A 32 0 SHEET 2 AA1 8 GLY A 38 ILE A 44 -1 O CYS A 42 N ASN A 26 SHEET 3 AA1 8 SER A 148 ILE A 151 -1 O LEU A 150 N ALA A 43 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 GLY A 54 VAL A 61 1 N THR A 59 O PHE A 90 SHEET 7 AA1 8 VAL A 169 TRP A 175 -1 O VAL A 169 N VAL A 60 SHEET 8 AA1 8 ASN A 26 SER A 32 -1 N LYS A 29 O LYS A 172 SHEET 1 AA2 2 THR A 127 MET A 128 0 SHEET 2 AA2 2 VAL B 2 ALA B 3 1 O ALA B 3 N THR A 127 SSBOND 1 CYS A 70 CYS A 98 1555 1555 2.04 CISPEP 1 SER A 32 PRO A 33 0 0.92 CRYST1 32.680 60.767 40.594 90.00 111.62 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 0.030600 0.000000 0.012128 0.00000 SCALE2 0.000000 0.016456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026499 0.00000