[English] 日本語
Yorodumi
- PDB-3jxs: Crystal structure of XG34, an evolved xyloglucan binding CBM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jxs
TitleCrystal structure of XG34, an evolved xyloglucan binding CBM
ComponentsXylanase
Keywordshydrolase / carbohydrate-binding domain / CBM / XYLOGLUCAN BINDING / CALCIUM BINDING / Xylan degradation
Function / homology
Function and homology information


xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Xylanase
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDivne, C. / Tan, T.-C. / Brumer, H. / Gullfot, F.
CitationJournal: Proteins / Year: 2009
Title: The crystal structure of XG-34, an evolved xyloglucan-specific carbohydrate-binding module.
Authors: Gullfot, F. / Tan, T.C. / von Schantz, L. / Karlsson, E.N. / Ohlin, M. / Brumer, H. / Divne, C.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylanase
B: Xylanase
C: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,03510
Polymers56,7173
Non-polymers3187
Water6,630368
1
A: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9863
Polymers18,9061
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0053
Polymers18,9061
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0454
Polymers18,9061
Non-polymers1393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.570, 43.760, 93.080
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Xylanase /


Mass: 18905.662 Da / Num. of mol.: 3 / Mutation: W279Y, E282H, F286L, F320H, Q321D, E322D, Y359F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: xg-34 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WTN6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium acetate, 30 % MPD, 0.02 M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03805 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2008 / Details: mirrors
RadiationMonochromator: bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03805 Å / Relative weight: 1
ReflectionResolution: 1.6→90.2 Å / Num. all: 61533 / Num. obs: 61533 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.037 / Net I/σ(I): 18.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 10127 / Rsym value: 0.518 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K45
Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.992 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21335 1251 2 %RANDOM
Rwork0.16948 ---
all0.17041 60282 --
obs0.17041 60282 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.739 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.46 Å2
2---0.64 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 13 368 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223903
X-RAY DIFFRACTIONr_bond_other_d0.0020.023363
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9215334
X-RAY DIFFRACTIONr_angle_other_deg1.93237800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61725.556189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9611512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214478
X-RAY DIFFRACTIONr_gen_planes_other00.02765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4761.52493
X-RAY DIFFRACTIONr_mcbond_other0.3941.51023
X-RAY DIFFRACTIONr_mcangle_it1.92424015
X-RAY DIFFRACTIONr_scbond_it2.95131410
X-RAY DIFFRACTIONr_scangle_it4.5024.51319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 82 -
Rwork0.254 4436 -
obs--99.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.12180.5638-0.20464.99681.6473.3990.04850.03610.07510.21110.03380.46650.0679-0.3327-0.08230.1381-0.0844-0.00350.16590.04890.1173-19.24559.856688.3033
24.17331.06880.42612.0672-0.3152.43110.1954-0.1068-0.22050.3989-0.1579-0.23070.31570.1909-0.03750.1539-0.025-0.05070.1020.00990.0305-5.238712.201893.903
31.55480.4241.72592.14510.18181.96450.1107-0.0267-0.02270.3234-0.1222-0.21970.05180.01590.01140.1535-0.0829-0.04090.2562-0.03970.06551.809420.356392.0234
42.54990.6687-0.47581.8235-0.48251.61490.1515-0.20480.08640.2169-0.07220.0158-0.06630.0414-0.07920.1246-0.0197-0.0090.1433-0.01420.085-4.329121.541689.0359
52.19870.53360.36192.7390.75992.33260.02240.0487-0.0683-0.0464-0.02460.2790.2453-0.28050.00210.0911-0.0572-0.00370.15470.00350.0958-18.473510.001479.7886
64.66282.4110.82845.3996-0.82950.5730.2109-0.72870.16560.6076-0.15670.1451-0.1677-0.2028-0.05430.1402-0.00030.09360.144-0.02560.1057-12.293427.762190.9781
71.60880.0995-0.56511.9088-0.29481.53670.0171-0.01120.0784-0.00550.0396-0.040.00190.0077-0.05670.0729-0.0078-0.0070.11620.01320.0787-8.932420.14477.4822
80.3501-0.7999-1.42385.16887.244214.53640.0362-0.08130.2462-0.02760.1198-0.1529-0.46060.2883-0.1560.1098-0.0090.02190.1295-0.06040.2633-9.816131.721483.19
91.59160.4818-0.10673.17481.44172.2550.0424-0.00970.0803-0.0935-0.02340.17370.0088-0.1497-0.01910.0734-0.02920.00120.12890.01580.0784-16.238116.190879.2063
101.77180.4475-0.35181.78630.19462.05610.0364-0.10730.11320.12570.01340.0154-0.04140.0177-0.04980.0908-0.0030.00650.1082-0.00890.0852-7.889422.784885.9194
110.8379-0.66780.06053.01220.8060.81040.1311-0.24560.18580.1094-0.0879-0.13850.2860.2661-0.04320.1210.07950.00150.4286-0.05620.088713.11213.619672.6359
123.2490.2037-2.38894.4944-1.85987.61510.0829-0.25060.12170.2627-0.1018-0.0063-0.03380.27870.01890.07380.0221-0.01310.1430.00220.07637.798813.690774.3262
132.8981-1.6950.28370.9994-0.07951.006-0.0294-0.1043-0.44290.07090.06180.25770.59340.0448-0.03240.37270.02380.00120.02620.03230.08150.65230.05572.2132
147.41380.5638-4.31231.1824-0.05255.0505-0.2184-0.5411-0.56310.0899-0.0847-0.5880.50210.49930.30310.15260.1488-0.04490.24360.08530.360721.41746.164169.354
152.20081.0691-1.12222.849-0.33491.5390.04350.1081-0.169-0.1695-0.1250.16340.46920.05920.08150.29040.0772-0.04060.0959-0.01420.04433.62873.155567.099
161.9377-1.11190.76361.4681-2.07896.72660.04050.12080.3869-0.0584-0.1058-0.0861-0.20630.12770.06530.05690.01080.01160.13380.03670.14135.347526.219461.5483
172.54110.09660.14763.6436-0.58071.9193-0.04160.2465-0.1418-0.2303-0.0453-0.15860.46460.22050.08690.1790.09550.02760.17490.00530.01828.77698.241359.448
182.50121.0781.02651.0597-0.50181.9954-0.04640.68710.0645-0.41320.18430.12910.63290.3467-0.13790.27790.0459-0.06390.3133-0.010.02183.32159.253155.5185
192.8974-1.84360.12863.1366-0.38361.85240.0590.1842-0.042-0.1859-0.06570.02670.1710.18640.00680.11170.02890.00350.18250.02570.11466.582717.787658.002
202.46520.7898-0.48472.53690.31371.4433-0.04230.2111-0.1595-0.3142-0.0836-0.0230.51120.18380.12590.29590.12590.03810.1585-0.00360.02178.43066.175162.4037
211.2806-0.20890.22622.20260.1591.40710.015-0.074-0.01510.2455-0.03920.22720.0363-0.08390.02420.0981-0.0020.0270.0888-0.01110.0868-21.712320.962466.6551
222.1887-0.5903-0.2672.2125-0.10082.00470.0538-0.04140.0970.0824-0.1632-0.1688-0.12010.21270.10950.0883-0.0018-0.03170.1255-0.01180.0972-12.296727.665159.5092
232.3440.5453-0.70122.0952-0.30031.29870.0144-0.07460.0560.1202-0.08250.2525-0.0819-0.05250.06810.08270.0097-0.01390.0789-0.01450.12-21.455229.802359.3282
241.9019-0.66620.35177.9379-0.8883.15320.04510.0174-0.19380.1863-0.03820.17020.202-0.0469-0.00690.08390.0012-0.0030.1042-0.0130.098-17.811610.861659.2648
250.9324-0.092-0.06034.89760.15460.8455-0.01440.03310.058-0.012-0.0330.4550.016-0.1460.04740.0754-0.0032-0.03560.0911-0.01730.1469-27.037216.627453.2341
264.618-3.9088-0.28718.9886-0.42931.6921-0.1259-0.07230.11890.00960.090.0954-0.0916-0.03470.03590.1331-0.0139-0.04170.1179-0.02860.0803-19.553922.916749.8617
2713.09341.11520.28152.97321.69642.3081-0.07010.34680.5395-0.2209-0.0681-0.1882-0.39290.24550.13820.1599-0.0313-0.0340.1390.03250.1396-14.238513.396647.5354
281.0075-0.3307-0.23583.84590.26430.5347-0.03230.12650.0796-0.4403-0.02530.4978-0.0417-0.13990.05760.09140.0185-0.09880.0644-0.00760.1377-27.177821.05448.1368
291.4434-0.19850.22794.4789-0.10160.71380.06980.098-0.125-0.1085-0.1306-0.17690.12930.11760.06070.09020.0117-0.00310.0897-0.01070.084-14.84513.662653.7515
301.28720.8538-0.61082.7143-0.69891.09140.0301-0.03010.0687-0.0557-0.0350.2686-0.017-0.06270.00490.04260.0168-0.03440.0746-0.0210.1091-24.175626.067154.1536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 31
3X-RAY DIFFRACTION3A32 - 47
4X-RAY DIFFRACTION4A48 - 74
5X-RAY DIFFRACTION5A75 - 89
6X-RAY DIFFRACTION6A90 - 95
7X-RAY DIFFRACTION7A96 - 117
8X-RAY DIFFRACTION8A118 - 123
9X-RAY DIFFRACTION9A124 - 142
10X-RAY DIFFRACTION10A143 - 166
11X-RAY DIFFRACTION11B1 - 22
12X-RAY DIFFRACTION12B23 - 29
13X-RAY DIFFRACTION13B30 - 42
14X-RAY DIFFRACTION14B43 - 54
15X-RAY DIFFRACTION15B55 - 75
16X-RAY DIFFRACTION16B76 - 86
17X-RAY DIFFRACTION17B87 - 109
18X-RAY DIFFRACTION18B110 - 123
19X-RAY DIFFRACTION19B124 - 142
20X-RAY DIFFRACTION20B143 - 166
21X-RAY DIFFRACTION21C1 - 25
22X-RAY DIFFRACTION22C26 - 38
23X-RAY DIFFRACTION23C39 - 72
24X-RAY DIFFRACTION24C73 - 81
25X-RAY DIFFRACTION25C82 - 95
26X-RAY DIFFRACTION26C96 - 109
27X-RAY DIFFRACTION27C110 - 115
28X-RAY DIFFRACTION28C116 - 134
29X-RAY DIFFRACTION29C135 - 148
30X-RAY DIFFRACTION30C149 - 166

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more