HEADER PROTEIN TRANSPORT 25-MAY-14 4TJV TITLE CRYSTAL STRUCTURE OF PROTEASE-ASSOCIATED DOMAIN OF ARABIDOPSIS TITLE 2 VACUOLAR SORTING RECEPTOR 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR-SORTING RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-182; COMPND 5 SYNONYM: ATVSR1,BP80-LIKE PROTEIN B,ATBP80B,EPIDERMAL GROWTH FACTOR COMPND 6 RECEPTOR-LIKE PROTEIN 1,ATELP1,SPOT 3 PROTEIN; COMPND 7 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 KEYWDS LIGAND-BINDING DOMAIN, BETA BARREL, APO FORM, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.LUO,Y.H.FONG,L.W.JIANG,K.B.WONG REVDAT 3 27-DEC-23 4TJV 1 REMARK REVDAT 2 22-NOV-17 4TJV 1 SOURCE JRNL REMARK REVDAT 1 10-DEC-14 4TJV 0 JRNL AUTH F.LUO,Y.H.FONG,Y.ZENG,J.SHEN,L.JIANG,K.B.WONG JRNL TITL HOW VACUOLAR SORTING RECEPTOR PROTEINS INTERACT WITH THEIR JRNL TITL 2 CARGO PROTEINS: CRYSTAL STRUCTURES OF APO AND CARGO-BOUND JRNL TITL 3 FORMS OF THE PROTEASE-ASSOCIATED DOMAIN FROM AN ARABIDOPSIS JRNL TITL 4 VACUOLAR SORTING RECEPTOR. JRNL REF PLANT CELL V. 26 3693 2014 JRNL REFN ESSN 1532-298X JRNL PMID 25271241 JRNL DOI 10.1105/TPC.114.129940 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.840 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 15966 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 798 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 33.7859 - 3.6707 1.00 2755 164 0.1564 0.1603 REMARK 3 2 3.6707 - 2.9141 1.00 2781 147 0.1643 0.1863 REMARK 3 3 2.9141 - 2.5459 0.99 2739 140 0.1824 0.1913 REMARK 3 4 2.5459 - 2.3131 0.99 2758 118 0.1730 0.2148 REMARK 3 5 2.3131 - 2.1474 0.98 2742 125 0.1630 0.1842 REMARK 3 6 2.1474 - 2.0208 0.98 2711 155 0.1553 0.1734 REMARK 3 7 2.0208 - 1.9196 0.97 2701 146 0.1559 0.2080 REMARK 3 8 1.9196 - 1.8360 0.97 2683 157 0.1638 0.2441 REMARK 3 9 1.8360 - 1.7654 0.96 2648 135 0.1742 0.2022 REMARK 3 10 1.7654 - 1.7045 0.96 2630 153 0.1809 0.2270 REMARK 3 11 1.7045 - 1.6512 0.95 2645 130 0.1980 0.2479 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.990 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 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 1285 REMARK 3 ANGLE : 1.352 1752 REMARK 3 CHIRALITY : 0.061 202 REMARK 3 PLANARITY : 0.008 227 REMARK 3 DIHEDRAL : 11.560 470 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 4TJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL 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) : 1.54 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 : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15984 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 33.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 15.50 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 74.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 15.20 REMARK 200 R MERGE FOR SHELL (I) : 0.14800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 36.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% GLYCEROL, 0.1 M MES PH 6.0, 30% REMARK 280 PEG 600, 5% (W/V) PEG 1000., VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 31.34000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 83 CG CD CE NZ REMARK 470 ARG A 86 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 SER A 32 143.40 -174.41 REMARK 500 SER A 32 146.84 -174.45 REMARK 500 PHE A 47 162.85 170.28 REMARK 500 ASP A 97 -20.78 73.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TJX RELATED DB: PDB DBREF 4TJV A 20 182 UNP P93026 VSR1_ARATH 20 182 SEQADV 4TJV GLY A 18 UNP P93026 EXPRESSION TAG SEQADV 4TJV 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 IOD A 201 1 HET IOD A 202 1 HET IOD A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 6(I 1-) FORMUL 8 HOH *137(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 ASP A 137 GLN A 142 1 6 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 TYR A 40 N LEU A 28 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 THR A 55 VAL A 61 1 N THR A 59 O PHE A 90 SHEET 7 AA1 8 ASN A 170 ASP A 174 -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 2.04 CISPEP 1 SER A 32 PRO A 33 0 0.96 CISPEP 2 SER A 32 PRO A 33 0 -0.46 SITE 1 AC1 1 LYS A 64 SITE 1 AC2 3 ASN A 26 PRO A 180 HIS A 181 SITE 1 AC3 4 GLU A 41 THR A 152 HOH A 415 HOH A 422 SITE 1 AC4 2 GLN A 142 HOH A 372 SITE 1 AC5 1 GLU A 177 SITE 1 AC6 2 SER A 19 HOH A 344 CRYST1 32.600 62.680 35.810 90.00 109.39 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 0.030675 0.000000 0.010796 0.00000 SCALE2 0.000000 0.015954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029604 0.00000