HEADER SUGAR BINDING PROTEIN 12-SEP-13 4MPI TITLE CRYSTAL STRUCTURE OF THE CHITIN-BINDING MODULE (CBM18) OF A CHITINASE- TITLE 2 LIKE PROTEIN FROM HEVEA BRASILIENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS I CHITINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CHITIN-BINDING DOMAIN (CBD18, UNP RESIDUES 1-43); COMPND 5 SYNONYM: CHITINASE-LIKE LECTIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEVEA BRASILIENSIS SUBSP. BRASILIENSIS; SOURCE 3 ORGANISM_TAXID: 187338; SOURCE 4 STRAIN: RIMM600; SOURCE 5 TISSUE: LATEX AND LEAVES; SOURCE 6 GENE: HBCHI-L1, LACIC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI DE3 PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS HEVEIN-LIKE DOMAIN, CHITIN OLIGOMERS, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.S.MARTINEZ-CABALLERO,J.A.HERMOSO,A.RODRIGUEZ-ROMERO REVDAT 3 20-SEP-23 4MPI 1 REMARK SEQADV REVDAT 2 15-OCT-14 4MPI 1 JRNL REVDAT 1 27-AUG-14 4MPI 0 JRNL AUTH S.MARTINEZ-CABALLERO,P.CANO-SANCHEZ,I.MARES-MEJIA, JRNL AUTH 2 A.G.DIAZ-SANCHEZ,M.L.MACIAS-RUBALCAVA,J.A.HERMOSO, JRNL AUTH 3 A.RODRIGUEZ-ROMERO JRNL TITL COMPARATIVE STUDY OF TWO GH19 CHITINASE-LIKE PROTEINS FROM JRNL TITL 2 HEVEA BRASILIENSIS, ONE EXHIBITING A NOVEL JRNL TITL 3 CARBOHYDRATE-BINDING DOMAIN. JRNL REF FEBS J. V. 281 4535 2014 JRNL REFN ISSN 1742-464X JRNL PMID 25104038 JRNL DOI 10.1111/FEBS.12962 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.3_1479) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11067 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 530 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 33.3622 - 2.5420 1.00 2684 119 0.1591 0.1910 REMARK 3 2 2.5420 - 2.0177 1.00 2619 146 0.1902 0.2363 REMARK 3 3 2.0177 - 1.7627 1.00 2643 131 0.1936 0.2106 REMARK 3 4 1.7627 - 1.6020 0.98 2591 134 0.2228 0.2696 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.65 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 : 0.006 660 REMARK 3 ANGLE : 1.108 880 REMARK 3 CHIRALITY : 0.033 80 REMARK 3 PLANARITY : 0.004 123 REMARK 3 DIHEDRAL : 15.823 242 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 4MPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN COOLED CHANNEL REMARK 200 -CUT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11117 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.602 REMARK 200 RESOLUTION RANGE LOW (A) : 33.355 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 21.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : 0.21600 REMARK 200 FOR SHELL : 4.900 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: PDB ENTRY 1Q9B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11 MG/ML PROTEIN, 0.1 M MES, PH 7.0, REMARK 280 1.6 M AMMONIUM SULFATE, 4% 1,4-DIOXANE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 33.64467 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 67.28933 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.46700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.11167 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 16.82233 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 ALA A -1 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 ALA A 7 48.60 -142.33 REMARK 500 ASN B 26 53.00 -119.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MST RELATED DB: PDB DBREF 4MPI A 1 43 UNP Q8GUD7 Q8GUD7_HEVBR 1 43 DBREF 4MPI B 1 43 UNP Q8GUD7 Q8GUD7_HEVBR 1 43 SEQADV 4MPI ALA A -1 UNP Q8GUD7 EXPRESSION TAG SEQADV 4MPI MET A 0 UNP Q8GUD7 EXPRESSION TAG SEQADV 4MPI ALA B -1 UNP Q8GUD7 EXPRESSION TAG SEQADV 4MPI MET B 0 UNP Q8GUD7 EXPRESSION TAG SEQRES 1 A 45 ALA MET GLU GLN CYS GLY ARG GLN ALA GLY GLY ALA LEU SEQRES 2 A 45 CYS PRO GLY GLY LEU CYS CYS SER GLN TYR GLY TRP CYS SEQRES 3 A 45 ALA ASN THR PRO GLU TYR CYS GLY SER GLY CYS GLN SER SEQRES 4 A 45 GLN CYS ASP GLY GLY VAL SEQRES 1 B 45 ALA MET GLU GLN CYS GLY ARG GLN ALA GLY GLY ALA LEU SEQRES 2 B 45 CYS PRO GLY GLY LEU CYS CYS SER GLN TYR GLY TRP CYS SEQRES 3 B 45 ALA ASN THR PRO GLU TYR CYS GLY SER GLY CYS GLN SER SEQRES 4 B 45 GLN CYS ASP GLY GLY VAL HET MES A 101 12 HET DIO B 101 6 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM DIO 1,4-DIETHYLENE DIOXIDE FORMUL 3 MES C6 H13 N O4 S FORMUL 4 DIO C4 H8 O2 FORMUL 5 HOH *85(H2 O) HELIX 1 1 CYS A 3 GLY A 8 5 6 HELIX 2 2 CYS A 12 LEU A 16 5 5 HELIX 3 3 THR A 27 GLY A 32 1 6 HELIX 4 4 CYS B 3 GLY B 8 5 6 HELIX 5 5 THR B 27 GLY B 32 1 6 SHEET 1 A 2 CYS A 17 CYS A 18 0 SHEET 2 A 2 CYS A 24 ALA A 25 -1 O ALA A 25 N CYS A 17 SHEET 1 B 2 CYS B 17 CYS B 18 0 SHEET 2 B 2 CYS B 24 ALA B 25 -1 O ALA B 25 N CYS B 17 SSBOND 1 CYS A 3 CYS A 18 1555 1555 2.03 SSBOND 2 CYS A 12 CYS A 24 1555 1555 2.03 SSBOND 3 CYS A 17 CYS A 31 1555 1555 2.04 SSBOND 4 CYS A 35 CYS A 39 1555 1555 2.03 SSBOND 5 CYS B 3 CYS B 18 1555 1555 2.04 SSBOND 6 CYS B 12 CYS B 24 1555 1555 2.03 SSBOND 7 CYS B 17 CYS B 31 1555 1555 2.04 SSBOND 8 CYS B 35 CYS B 39 1555 1555 2.05 SITE 1 AC1 6 MET A 0 TRP A 23 PRO A 28 MET B 0 SITE 2 AC1 6 TRP B 23 PRO B 28 SITE 1 AC2 3 PRO B 13 GLY B 14 HOH B 239 CRYST1 38.515 38.515 100.934 90.00 90.00 120.00 P 61 12 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 0.025964 0.014990 0.000000 0.00000 SCALE2 0.000000 0.029981 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009907 0.00000