HEADER PLANT PROTEIN 29-JUN-15 5C9Y TITLE CRYSTAL STRUCTURE OF YELLOW LUPINE LLPR-10.1A PROTEIN PARTIALLY TITLE 2 SATURATED WITH TRANS-ZEATIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN LLR18A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LLPR10.1A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUPINUS LUTEUS; SOURCE 3 ORGANISM_COMMON: EUROPEAN YELLOW LUPIN; SOURCE 4 ORGANISM_TAXID: 3873; SOURCE 5 GENE: LLR18A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-3A KEYWDS PR-10 FOLD, LIGAND BINDING, PHYTOHORMONE BINDING PROTEIN, TRANS- KEYWDS 2 ZEATIN, CYTOKININ, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SLIWIAK,M.M.SIKORSKI,M.JASKOLSKI REVDAT 5 10-JAN-24 5C9Y 1 REMARK REVDAT 4 17-JUL-19 5C9Y 1 REMARK REVDAT 3 13-JAN-16 5C9Y 1 JRNL REVDAT 2 23-DEC-15 5C9Y 1 JRNL REVDAT 1 09-DEC-15 5C9Y 0 JRNL AUTH J.SLIWIAK,R.DOLOT,K.MICHALSKA,K.SZPOTKOWSKI,G.BUJACZ, JRNL AUTH 2 M.SIKORSKI,M.JASKOLSKI JRNL TITL CRYSTALLOGRAPHIC AND CD PROBING OF LIGAND-INDUCED JRNL TITL 2 CONFORMATIONAL CHANGES IN A PLANT PR-10 PROTEIN. JRNL REF J.STRUCT.BIOL. V. 193 55 2016 JRNL REFN ESSN 1095-8657 JRNL PMID 26644353 JRNL DOI 10.1016/J.JSB.2015.11.008 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1-743 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 0.0000 - 1.5000 0.00 0 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 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 : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FLAT POSTIVE ELECTRON DENSITIES COULD REMARK 3 BE OBSERVED IN THE STRUCTURE INDICATING THE PRESENCE OF PURING REMARK 3 RINGS AND TAILS OF THREE TRANS-ZEATIN MOLECULES: TWO INSIDE REMARK 3 PROTEIN CAVITY (ONE INTERACTING WITH TYR82 AND OTHER WITH SER101) REMARK 3 AND ONE ON THE SURFACE OF PROTEIN (STAYING IN CONTACT WITH REMARK 3 GLU35). HOWEVER THEY POSSESS DISCONTINUITIES AND ARE REMARK 3 INSUFFICIENT FOR PROPER LIGAND MODELING THUS THE STRUCTURE IS REMARK 3 DEPOSITED WITHOUT LIGAND MOLECULES IN ITS COORDINATES ALTHOUGH REMARK 3 TRANS-ZEATIN WAS PRESENT IN CRYSTALLIZATION CONDINTIONS. REMARK 4 REMARK 4 5C9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000209334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81738 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR555 FLAT PANEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21584 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.160 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.16 REMARK 200 R MERGE FOR SHELL (I) : 0.82900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.450 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: 1ICX REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M (NH4)2SO4, 0.1 M MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 17.75300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.23800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.95900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.23800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.75300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.95900 REMARK 290 SMTRY3 4 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 69 CE NZ REMARK 470 GLN A 133 CG CD OE1 NE2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 PHE A 136 CG CD1 CD2 CE1 CE2 CZ 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 286 O HOH A 324 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 8 NZ LYS A 32 2554 2.07 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 THR A 23 -86.52 -118.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 5C9Y A 1 155 UNP P52778 L18A_LUPLU 2 156 SEQRES 1 A 155 GLY ILE PHE ALA PHE GLU ASN GLU GLN SER SER THR VAL SEQRES 2 A 155 ALA PRO ALA LYS LEU TYR LYS ALA LEU THR LYS ASP SER SEQRES 3 A 155 ASP GLU ILE VAL PRO LYS VAL ILE GLU PRO ILE GLN SER SEQRES 4 A 155 VAL GLU ILE VAL GLU GLY ASN GLY GLY PRO GLY THR ILE SEQRES 5 A 155 LYS LYS ILE ILE ALA ILE HIS ASP GLY HIS THR SER PHE SEQRES 6 A 155 VAL LEU HIS LYS LEU ASP ALA ILE ASP GLU ALA ASN LEU SEQRES 7 A 155 THR TYR ASN TYR SER ILE ILE GLY GLY GLU GLY LEU ASP SEQRES 8 A 155 GLU SER LEU GLU LYS ILE SER TYR GLU SER LYS ILE LEU SEQRES 9 A 155 PRO GLY PRO ASP GLY GLY SER ILE GLY LYS ILE ASN VAL SEQRES 10 A 155 LYS PHE HIS THR LYS GLY ASP VAL LEU SER GLU THR VAL SEQRES 11 A 155 ARG ASP GLN ALA LYS PHE LYS GLY LEU GLY LEU PHE LYS SEQRES 12 A 155 ALA ILE GLU GLY TYR VAL LEU ALA HIS PRO ASP TYR FORMUL 2 HOH *144(H2 O) HELIX 1 AA1 ALA A 14 THR A 23 1 10 HELIX 2 AA2 ASP A 25 ILE A 34 1 10 HELIX 3 AA3 GLU A 75 ASN A 77 5 3 HELIX 4 AA4 PRO A 107 GLY A 109 5 3 HELIX 5 AA5 SER A 127 HIS A 152 1 26 SHEET 1 AA1 7 ILE A 2 SER A 11 0 SHEET 2 AA1 7 SER A 111 THR A 121 -1 O SER A 111 N SER A 11 SHEET 3 AA1 7 LEU A 94 PRO A 105 -1 N SER A 98 O LYS A 118 SHEET 4 AA1 7 THR A 79 GLY A 86 -1 N TYR A 82 O TYR A 99 SHEET 5 AA1 7 HIS A 62 ASP A 74 -1 N ALA A 72 O ASN A 81 SHEET 6 AA1 7 ILE A 52 HIS A 59 -1 N ILE A 55 O VAL A 66 SHEET 7 AA1 7 ILE A 37 GLU A 44 -1 N GLU A 41 O LYS A 54 CRYST1 35.506 57.918 62.476 90.00 90.00 90.00 P 21 21 21 4 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 0.028164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016006 0.00000