HEADER HYDROLASE 09-SEP-20 7K2Z TITLE CRYSTAL STRUCTURE OF PISUM SATIVUM KAI2 APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSKAI2B PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 3 ORGANISM_TAXID: 3888; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME, KARRIKIN, RECEPTOR, A/B HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.GUERCIO,N.SHABEK REVDAT 4 18-OCT-23 7K2Z 1 REMARK REVDAT 3 02-MAR-22 7K2Z 1 JRNL REVDAT 2 23-FEB-22 7K2Z 1 JRNL REVDAT 1 16-FEB-22 7K2Z 0 JRNL AUTH A.M.GUERCIO,S.TORABI,D.CORNU,M.DALMAIS,A.BENDAHMANE, JRNL AUTH 2 C.LE SIGNOR,J.P.PILLOT,P.LE BRIS,F.D.BOYER,C.RAMEAU, JRNL AUTH 3 C.GUTJAHR,A.DE SAINT GERMAIN,N.SHABEK JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSES EXPLAIN PEA KAI2 RECEPTOR JRNL TITL 2 DIVERSITY AND REVEAL STEREOSELECTIVE CATALYSIS DURING SIGNAL JRNL TITL 3 PERCEPTION. JRNL REF COMMUN BIOL V. 5 126 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 35149763 JRNL DOI 10.1038/S42003-022-03085-6 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 34306 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 4.3470 - 3.8700 1.00 2404 149 0.1484 0.1569 REMARK 3 2 3.8700 - 3.0700 1.00 2347 146 0.1431 0.1513 REMARK 3 3 3.0700 - 2.6900 1.00 2342 144 0.1561 0.1926 REMARK 3 4 2.6900 - 2.4400 1.00 2334 145 0.1549 0.1719 REMARK 3 5 2.4400 - 2.2700 1.00 2348 145 0.1520 0.1731 REMARK 3 6 2.2700 - 2.1300 1.00 2324 143 0.1487 0.1803 REMARK 3 7 2.1300 - 2.0300 1.00 2328 145 0.1515 0.1971 REMARK 3 8 2.0300 - 1.9400 1.00 2336 144 0.1579 0.1985 REMARK 3 9 1.9400 - 1.8600 1.00 2339 146 0.1644 0.2076 REMARK 3 10 1.8600 - 1.8000 1.00 2327 144 0.1756 0.2278 REMARK 3 11 1.8000 - 1.7400 1.00 2318 143 0.1743 0.2131 REMARK 3 12 1.7400 - 1.6900 1.00 2329 144 0.1822 0.2166 REMARK 3 13 1.6900 - 1.6500 1.00 2314 144 0.2016 0.2232 REMARK 3 14 1.6500 - 1.6100 0.83 1916 118 0.2366 0.2745 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.37 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: NULL REMARK 4 REMARK 4 7K2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 43.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: PHENIX REMARK 200 STARTING MODEL: 5Z9H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 2.75% PEG 2000, REMARK 280 2.75% PEG 3350, 2.75% PEG 4000, 2.75% PEG-ME 5000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 43.79750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.57300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.79750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.57300 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 607 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 743 LIES ON A SPECIAL POSITION. 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 28 -162.67 -124.19 REMARK 500 SER A 95 -124.53 51.99 REMARK 500 ARG A 123 128.85 -171.24 REMARK 500 ASN A 149 89.69 -156.69 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 779 DISTANCE = 7.86 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 400 DBREF 7K2Z A 1 270 PDB 7K2Z 7K2Z 1 270 SEQRES 1 A 270 MET GLY ILE VAL GLU GLU ALA HIS ASN VAL LYS VAL LEU SEQRES 2 A 270 GLY THR GLY SER ARG PHE ILE VAL LEU ALA HIS GLY PHE SEQRES 3 A 270 GLY THR ASP GLN SER VAL TRP LYS HIS LEU VAL PRO HIS SEQRES 4 A 270 LEU LEU GLU GLU PHE ARG VAL ILE LEU TYR ASP ASN MET SEQRES 5 A 270 GLY ALA GLY THR THR ASN PRO ASP TYR PHE ASP PHE GLU SEQRES 6 A 270 ARG TYR SER THR LEU GLU GLY TYR ALA TYR ASP LEU LEU SEQRES 7 A 270 ALA ILE LEU GLN GLU LEU ARG VAL ASP SER CYS ILE PHE SEQRES 8 A 270 VAL GLY HIS SER VAL SER ALA MET ILE GLY THR VAL ALA SEQRES 9 A 270 SER ILE SER ARG PRO ASP LEU PHE ALA LYS ILE ILE MET SEQRES 10 A 270 ILE SER ALA SER PRO ARG TYR LEU ASN ASP SER ASN TYR SEQRES 11 A 270 PHE GLY GLY PHE GLU GLN GLU ASP LEU ASP GLN LEU PHE SEQRES 12 A 270 ASN ALA MET ALA SER ASN TYR LYS ALA TRP CYS SER GLY SEQRES 13 A 270 PHE ALA PRO MET ALA ILE GLY GLY ASP MET GLU SER VAL SEQRES 14 A 270 ALA VAL GLN GLU PHE SER ARG THR LEU PHE ASN MET ARG SEQRES 15 A 270 PRO ASP ILE ALA LEU SER VAL LEU GLN THR ILE PHE LYS SEQRES 16 A 270 SER ASP MET ARG GLN ILE LEU CYS LEU VAL SER VAL PRO SEQRES 17 A 270 CYS HIS ILE ILE GLN SER MET LYS ASP LEU ALA VAL PRO SEQRES 18 A 270 VAL VAL VAL ALA GLU TYR LEU HIS GLN HIS VAL GLY THR SEQRES 19 A 270 GLU SER ILE VAL GLU VAL MET SER THR GLU GLY HIS LEU SEQRES 20 A 270 PRO GLN LEU SER SER PRO ASP VAL VAL ILE PRO VAL ILE SEQRES 21 A 270 LEU LYS HIS ILE ARG TYR ASP ILE VAL ALA HET GOL A 400 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *279(H2 O) HELIX 1 AA1 GLY A 2 HIS A 8 1 7 HELIX 2 AA2 ASP A 29 LYS A 34 5 6 HELIX 3 AA3 LEU A 36 LEU A 40 5 5 HELIX 4 AA4 ASN A 58 PHE A 62 5 5 HELIX 5 AA5 THR A 69 LEU A 84 1 16 HELIX 6 AA6 SER A 95 ARG A 108 1 14 HELIX 7 AA7 GLU A 135 ASN A 149 1 15 HELIX 8 AA8 ASN A 149 GLY A 163 1 15 HELIX 9 AA9 SER A 168 ASN A 180 1 13 HELIX 10 AB1 ARG A 182 LYS A 195 1 14 HELIX 11 AB2 MET A 198 VAL A 205 5 8 HELIX 12 AB3 PRO A 221 VAL A 232 1 12 HELIX 13 AB4 LEU A 247 SER A 252 1 6 HELIX 14 AB5 SER A 252 TYR A 266 1 15 SHEET 1 AA1 7 LYS A 11 LEU A 13 0 SHEET 2 AA1 7 PHE A 44 TYR A 49 -1 O VAL A 46 N LEU A 13 SHEET 3 AA1 7 ARG A 18 ALA A 23 1 N ILE A 20 O ILE A 47 SHEET 4 AA1 7 CYS A 89 HIS A 94 1 O VAL A 92 N VAL A 21 SHEET 5 AA1 7 PHE A 112 ILE A 118 1 O ILE A 116 N PHE A 91 SHEET 6 AA1 7 CYS A 209 LYS A 216 1 O HIS A 210 N MET A 117 SHEET 7 AA1 7 SER A 236 GLU A 244 1 O MET A 241 N GLN A 213 SITE 1 AC1 6 SER A 95 TYR A 124 ILE A 193 HIS A 246 SITE 2 AC1 6 HOH A 529 HOH A 602 CRYST1 87.595 71.146 49.065 90.00 117.62 90.00 C 1 2 1 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 0.011416 0.000000 0.005974 0.00000 SCALE2 0.000000 0.014056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023003 0.00000