HEADER ALLERGEN 08-OCT-22 8H3I TITLE CRYSTAL STRUCTURE OF THE APO-FORM PATHOGENESIS-RELATED PROTEIN HCPR10 TITLE 2 FROM HALOSTACHYS CASPICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR10; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOSTACHYS CASPICA; SOURCE 3 ORGANISM_TAXID: 282322; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PATHOGENESIS-RELATED PROTEIN, HALOSTACHYS CASPICA, RESERVOIR FOR KEYWDS 2 CYTOKININ, ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR Z.WANG,Y.REN REVDAT 3 01-MAY-24 8H3I 1 JRNL REVDAT 2 08-NOV-23 8H3I 1 REMARK REVDAT 1 17-MAY-23 8H3I 0 JRNL AUTH Y.FENG,Y.REN,H.ZHANG,Y.HENG,Z.WANG,Y.WANG JRNL TITL HALOSTACHYS CASPICA PATHOGENESIS-RELATED PROTEIN 10 ACTS AS JRNL TITL 2 A CYTOKININ RESERVOIR TO REGULATE PLANT GROWTH AND JRNL TITL 3 DEVELOPMENT. JRNL REF FRONT PLANT SCI V. 14 16985 2023 JRNL REFN ESSN 1664-462X JRNL PMID 37180382 JRNL DOI 10.3389/FPLS.2023.1116985 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.FENG,Y.REN,H.ZHANG,Y.HENG,Z.WANG,Y.WANG REMARK 1 TITL HALOSTACHYS CASPICA PATHOGENESIS-RELATED PROTEIN 10 ACTS AS REMARK 1 TITL 2 A CYTOKININ RESERVOIR TO REGULATE PLANT GROWTH AND REMARK 1 TITL 3 DEVELOPMENT REMARK 1 REF FRONT PLANT SCI V. 14 16985 2023 REMARK 1 REFN ESSN 1664-462X REMARK 1 DOI HTTPS://DOI.ORG/10.3389/FPLS.2023.1116985 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15324 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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 22.4600 - 3.4500 1.00 2557 123 0.1800 0.2208 REMARK 3 2 3.4500 - 2.7400 1.00 2448 124 0.2125 0.2367 REMARK 3 3 2.7400 - 2.3900 1.00 2415 121 0.2149 0.2954 REMARK 3 4 2.3900 - 2.1700 1.00 2374 147 0.2107 0.2622 REMARK 3 5 2.1700 - 2.0200 1.00 2407 114 0.2064 0.2731 REMARK 3 6 2.0200 - 1.9000 1.00 2349 145 0.2094 0.2804 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) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.31 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 : 0.011 1302 REMARK 3 ANGLE : 1.097 1768 REMARK 3 CHIRALITY : 0.105 197 REMARK 3 PLANARITY : 0.007 231 REMARK 3 DIHEDRAL : 23.514 475 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 8H3I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 12-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300032717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15377 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 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) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66000 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: 1BV1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES SODIUM 7.5;1.4M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.34867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.67433 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.67433 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.34867 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 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 261 LIES ON A SPECIAL POSITION. 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 -1 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 272 O HOH A 284 2.08 REMARK 500 O HOH A 289 O HOH A 293 2.13 REMARK 500 O HOH A 213 O HOH A 255 2.18 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 ASP A 96 -29.51 -35.23 REMARK 500 TYR A 100 133.68 -172.80 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8H3I A 1 161 UNP A0A171NYA8_9CARY DBREF2 8H3I A A0A171NYA8 1 161 SEQADV 8H3I GLY A -1 UNP A0A171NYA EXPRESSION TAG SEQADV 8H3I SER A 0 UNP A0A171NYA EXPRESSION TAG SEQRES 1 A 163 GLY SER MET GLY VAL PHE THR CYS THR LEU ALA ASP ILE SEQRES 2 A 163 THR SER PRO VAL ALA PRO ALA ARG LEU PHE GLN ALA PHE SEQRES 3 A 163 THR ILE ASP ASN HIS ASN LEU MET PRO LYS VAL VAL PRO SEQRES 4 A 163 GLN PHE VAL LYS SER ILE ASP PHE VAL GLN GLY ASP SER SEQRES 5 A 163 THR ALA VAL GLY CYS VAL LYS GLN ILE ASN PHE PRO ALA SEQRES 6 A 163 ASP ALA PRO PHE THR TYR VAL LYS ASN ARG VAL ASP GLU SEQRES 7 A 163 ILE ASP ALA SER LYS TYR TYR LEU LYS TYR THR CYS ILE SEQRES 8 A 163 GLU GLY ASP ALA PHE PRO ASP THR VAL GLU TYR ALA VAL SEQRES 9 A 163 TYR GLU ASP THR PHE GLU GLN THR GLU THR GLY SER ARG SEQRES 10 A 163 CYS LYS MET VAL ALA HIS TYR HIS LEU LYS GLY ASP SER SEQRES 11 A 163 VAL MET LYS GLU GLU ASP VAL ALA PRO ALA LYS GLU GLY SEQRES 12 A 163 ILE GLN LYS MET PHE LYS ALA VAL GLU GLU HIS LEU ILE SEQRES 13 A 163 ALA ASN PRO GLN LEU TYR ALA FORMUL 2 HOH *93(H2 O) HELIX 1 AA1 ALA A 16 ILE A 26 1 11 HELIX 2 AA2 ASP A 27 VAL A 36 1 10 HELIX 3 AA3 ALA A 79 LYS A 81 5 3 HELIX 4 AA4 LYS A 131 ASN A 156 1 26 SHEET 1 AA1 7 GLY A 2 SER A 13 0 SHEET 2 AA1 7 SER A 114 LEU A 124 -1 O CYS A 116 N ILE A 11 SHEET 3 AA1 7 VAL A 98 GLN A 109 -1 N VAL A 102 O HIS A 121 SHEET 4 AA1 7 TYR A 83 GLY A 91 -1 N TYR A 86 O TYR A 103 SHEET 5 AA1 7 TYR A 69 ASP A 78 -1 N ARG A 73 O THR A 87 SHEET 6 AA1 7 VAL A 56 ASN A 60 -1 N LYS A 57 O ASN A 72 SHEET 7 AA1 7 SER A 42 GLN A 47 -1 N ASP A 44 O GLN A 58 CRYST1 59.426 59.426 92.023 90.00 90.00 120.00 P 32 2 1 6 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 0.016828 0.009715 0.000000 0.00000 SCALE2 0.000000 0.019431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010867 0.00000