HEADER PROTEIN TRANSPORT 25-MAY-14 4TJX TITLE CRYSTAL STRUCTURE OF PROTEASE-ASSOCIATED DOMAIN OF ARABIDOPSIS VSR1 IN TITLE 2 COMPLEX WITH ALEURAIN PEPTIDE 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ALEURAIN 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: HORDEUM VULGARE; SOURCE 11 ORGANISM_TAXID: 4513 KEYWDS COMPLEX STRUCTURE, LIGAND-BINDING DOMAIN, ALEURAIN PEPETIDE, BETA- KEYWDS 2 BARREL, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.LUO,Y.H.FONG,L.W.JIANG,K.B.WONG REVDAT 2 27-SEP-23 4TJX 1 SOURCE JRNL REMARK REVDAT 1 10-DEC-14 4TJX 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 10221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1013 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 36.5874 - 3.6365 0.99 1401 153 0.1618 0.1703 REMARK 3 2 3.6365 - 2.8868 0.97 1370 153 0.1451 0.2097 REMARK 3 3 2.8868 - 2.5220 0.96 1351 151 0.1564 0.2070 REMARK 3 4 2.5220 - 2.2914 0.94 1305 146 0.1541 0.2105 REMARK 3 5 2.2914 - 2.1272 0.93 1295 135 0.1496 0.2065 REMARK 3 6 2.1272 - 2.0018 0.92 1290 144 0.1485 0.2304 REMARK 3 7 2.0018 - 1.9020 0.88 1196 131 0.1627 0.2437 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.970 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 : 0.006 1203 REMARK 3 ANGLE : 1.040 1632 REMARK 3 CHIRALITY : 0.066 189 REMARK 3 PLANARITY : 0.004 208 REMARK 3 DIHEDRAL : 10.375 438 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): 5.7622 32.3256 9.9638 REMARK 3 T TENSOR REMARK 3 T11: 0.0977 T22: 0.1111 REMARK 3 T33: 0.0382 T12: -0.0062 REMARK 3 T13: -0.0291 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.6136 L22: 0.5311 REMARK 3 L33: 0.9104 L12: -0.0722 REMARK 3 L13: -0.1864 L23: 0.4573 REMARK 3 S TENSOR REMARK 3 S11: 0.0201 S12: -0.0236 S13: -0.0105 REMARK 3 S21: -0.0004 S22: -0.0235 S23: 0.0126 REMARK 3 S31: 0.0462 S32: -0.0229 S33: -0.0016 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 4TJX 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_1000201736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 36.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.13400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 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: 4TJV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 25% PEG 6000, REMARK 280 VAPOR DIFFUSION, HANGING 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 29.28100 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: 470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 PRO B 5 REMARK 465 ILE B 6 REMARK 465 ARG B 7 REMARK 465 PRO B 8 REMARK 465 VAL B 9 REMARK 465 THR B 10 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 ASN B 4 CA C O CB CG OD1 ND2 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 240 O HOH A 272 2.10 REMARK 500 O HOH A 235 O HOH A 240 2.17 REMARK 500 O HOH A 257 O HOH A 345 2.19 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 ASN A 46 33.07 -83.09 REMARK 500 ASP A 97 -30.94 74.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 355 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 356 DISTANCE = 6.94 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TJV RELATED DB: PDB DBREF 4TJX A 20 182 UNP P93026 VSR1_ARATH 20 182 DBREF 4TJX B 1 10 PDB 4TJX 4TJX 1 10 SEQADV 4TJX GLY A 18 UNP P93026 EXPRESSION TAG SEQADV 4TJX 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 10 ALA ASP SER ASN PRO ILE ARG PRO VAL THR FORMUL 3 HOH *160(H2 O) HELIX 1 AA1 PRO A 33 LYS A 37 5 5 HELIX 2 AA2 TYR A 73 ASP A 77 5 5 HELIX 3 AA3 TYR A 99 ALA A 110 1 12 HELIX 4 AA4 TYR A 140 ILE A 144 5 5 HELIX 5 AA5 THR A 152 GLY A 165 1 14 SHEET 1 AA1 8 LYS A 25 SER A 32 0 SHEET 2 AA1 8 GLY A 38 ILE A 44 -1 O TYR A 40 N LEU A 28 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 THR A 55 VAL A 61 1 N THR A 59 O PHE A 90 SHEET 7 AA1 8 VAL A 169 ASP A 174 -1 O VAL A 169 N VAL A 60 SHEET 8 AA1 8 LYS A 25 SER A 32 -1 N LYS A 29 O LYS A 172 SSBOND 1 CYS A 70 CYS A 98 1555 1555 2.07 CISPEP 1 SER A 32 PRO A 33 0 -0.60 CRYST1 32.513 58.562 36.583 90.00 90.65 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 0.030757 0.000000 0.000349 0.00000 SCALE2 0.000000 0.017076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027337 0.00000