HEADER PLANT PROTEIN 24-SEP-24 9GVH TITLE CRYSTAL STRUCTURE OF CHITIN BINDING PROTEIN FROM IBERIS UMBELLATA L. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITIN BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: CHITIN BINDING PROTEIN; COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: IBERIS UMBELLATA; SOURCE 3 ORGANISM_TAXID: 226049; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: IBERIS UMBELLATA; SOURCE 6 ORGANISM_TAXID: 226049 KEYWDS CHITIN BINDING PROTEIN, 2S ALBUMIN, PLANT LIPID TRANSFER PROTEIN, KEYWDS 2 SEED STORAGE HELICAL DOMAIN-CONTAINING PROTEIN., PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SAEED,C.BETZEL,H.BROGNARO,B.ALVES FRANCA,S.MEHMOOD,P.RAJAIAH AUTHOR 2 PRABHU,U.ISHAQ,A.AKREM REVDAT 2 25-DEC-24 9GVH 1 JRNL REVDAT 1 11-DEC-24 9GVH 0 JRNL AUTH A.SAEED,C.BETZEL,H.BROGNARO,B.ALVES FRANCA,S.MEHMOOD, JRNL AUTH 2 P.RAJAIAH PRABHU,U.ISHAQ,A.AKREM JRNL TITL CRYSTAL STRUCTURE OF CHITIN BINDING PROTEIN FROM IBERIS JRNL TITL 2 UMBELLATA L. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23897 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 : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1184 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 28.7400 - 2.6800 1.00 3014 157 0.1742 0.1829 REMARK 3 2 2.6800 - 2.1300 1.00 2863 156 0.1548 0.2107 REMARK 3 3 2.1300 - 1.8600 1.00 2841 148 0.1351 0.1830 REMARK 3 4 1.8600 - 1.6900 1.00 2815 139 0.1314 0.1725 REMARK 3 5 1.6900 - 1.5700 1.00 2811 129 0.1329 0.1938 REMARK 3 6 1.5700 - 1.4800 1.00 2805 142 0.1316 0.2110 REMARK 3 7 1.4800 - 1.4000 1.00 2784 160 0.1496 0.2044 REMARK 3 8 1.4000 - 1.3400 1.00 2780 153 0.1912 0.2488 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.133 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.675 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.18 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 : 0.014 899 REMARK 3 ANGLE : 1.252 1213 REMARK 3 CHIRALITY : 0.101 130 REMARK 3 PLANARITY : 0.015 164 REMARK 3 DIHEDRAL : 12.793 322 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 9GVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976210 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23901 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 28.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.250 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 0.2M SODIUM REMARK 280 NITRATE OR AMMONIUM NITRATE/LITHIUM NITRATE/POTASIUM NITRATE 16- REMARK 280 20MG PROTEIN IN 50MM SODIUM ACETATE, 150MM SODIUM CHLORIDE, PH REMARK 280 4.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 22.56750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.61750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.56750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.61750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 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 B 332 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 23 CG1 - CB - CG2 ANGL. DEV. = -14.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9GVH A -1 33 PDB 9GVH 9GVH -1 33 DBREF 9GVH B 56 130 PDB 9GVH 9GVH 56 130 SEQRES 1 A 35 PRO GLY PRO PHE GLY PRO ARG PRO SER CYS PRO SER GLN SEQRES 2 A 35 PHE VAL SER ALA HIS ARG LEU SER ALA CYS GLN ILE TRP SEQRES 3 A 35 ILE HIS LYS GLU ALA VAL SER SER GLY SEQRES 1 B 75 GLY GLY GLU ARG PRO PRO LEU LEU ARG LEU CYS CYS THR SEQRES 2 B 75 GLN LEU HIS LEU GLN ASN PRO GLN CYS VAL CYS MET THR SEQRES 3 B 75 LEU ARG ARG ALA ALA GLN ALA VAL ARG SER ARG GLN GLY SEQRES 4 B 75 ILE SER ALA SER SER GLN VAL GLN ARG LEU PHE GLU THR SEQRES 5 B 75 ALA ARG HIS LEU PRO ALA THR CYS ASN PHE SER GLN VAL SEQRES 6 B 75 GLY VAL CYS PRO PHE THR ALA ILE PRO ALA HET NO3 A 101 4 HET NO3 A 102 4 HET ACY A 103 4 HET SO4 A 104 5 HET NO3 A 105 4 HET ACY B 201 4 HET LI B 202 1 HET NO3 B 203 4 HET NO3 B 204 4 HET NO3 B 205 4 HET ACY B 206 4 HET SO4 B 207 5 HET SO4 B 208 5 HETNAM NO3 NITRATE ION HETNAM ACY ACETIC ACID HETNAM SO4 SULFATE ION HETNAM LI LITHIUM ION FORMUL 3 NO3 6(N O3 1-) FORMUL 5 ACY 3(C2 H4 O2) FORMUL 6 SO4 3(O4 S 2-) FORMUL 9 LI LI 1+ FORMUL 16 HOH *56(H2 O) HELIX 1 AA1 SER A 7 ALA A 15 1 9 HELIX 2 AA2 LEU A 18 SER A 31 1 14 HELIX 3 AA3 PRO B 60 HIS B 71 1 12 HELIX 4 AA4 LEU B 72 GLN B 73 5 2 HELIX 5 AA5 ASN B 74 GLN B 76 5 3 HELIX 6 AA6 CYS B 77 GLY B 94 1 18 HELIX 7 AA7 ALA B 97 CYS B 115 1 19 SSBOND 1 CYS A 8 CYS B 77 1555 1555 2.02 SSBOND 2 CYS A 21 CYS B 66 1555 1555 2.05 SSBOND 3 CYS B 67 CYS B 115 1555 1555 2.06 SSBOND 4 CYS B 79 CYS B 123 1555 1555 2.03 LINK LI LI B 202 O HOH B 325 1555 1555 2.37 CRYST1 45.135 73.235 31.250 90.00 90.00 90.00 P 21 21 2 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 0.022156 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032000 0.00000