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Database: PDB / ID: 2wze
TitleHigh resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose
ComponentsENDO-1,4-BETA-XYLANASE Y
KeywordsHYDROLASE / XYLAN DEGRADATION / CELLULOSOME / GLYCOSIDASE
Function / homology
Function and homology information


cellulosome / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4beta-beta-xylotriose / PHOSPHATE ION / Endo-1,4-beta-xylanase Y
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsNajmudin, S. / Pinheiro, B.A. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A.
Citation
Journal: J.Struct.Biol. / Year: 2010
Title: Putting an N-Terminal End to the Clostridium Thermocellum Xylanase Xyn10B Story: Crystal Structure of the Cbm22-1-Gh10 Modules Complexed with Xylohexaose.
Authors: Najmudin, S. / Pinheiro, B.A. / Prates, J.A.M. / Gilbert, H.J. / Romao, M.J. / Fontes, C.M.G.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Purification, Crystallization and Crystallographic Analysis of Clostridium Thermocellum Endo-1,4-Beta- D-Xylanase 10B in Complex with Xylohexaose.
Authors: Najmudin, S. / Pinheiro, B.A. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A.
History
DepositionNov 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE Y
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,52020
Polymers121,3172
Non-polymers2,20418
Water16,826934
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A: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,76010
Polymers60,6581
Non-polymers1,1029
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,76010
Polymers60,6581
Non-polymers1,1029
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.037, 173.037, 136.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2130-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ENDO-1,4-BETA-XYLANASE Y / XYLANASE Y / 1\ / 4-BETA-D-XYLAN XYLANOHYDROLASE Y / XYLY / ENDO-1\ / 4-BETA-D-XYLANASE 10B


Mass: 60658.254 Da / Num. of mol.: 2 / Fragment: CBM22-1, GH10, RESIDUES 33-551 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 2 XYLOHEXAOSES (BUT ONLY 3 OF THE 6 XYLOSE RINGS CAN BE SEEN IN THE ELECTRON DENSITY), 2 PHOSPHATE, 2 CALCIUM IONS AND 12 GLYCEROL MOLECULES.
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: YS / Plasmid: PGEM T-EASY AND PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): METHIONINE AUXOTROPH B834(DE3) / References: UniProt: P51584, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 950 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 934 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 337 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 337 TO ALA
Has protein modificationY
Nonpolymer detailsPHOSPHATE ION (PO4): FROM CRYSTALLIZATION BUFFER GLYCEROL (GOL): FROM CRYOPROTECTANT CALCIUM ION ...PHOSPHATE ION (PO4): FROM CRYSTALLIZATION BUFFER GLYCEROL (GOL): FROM CRYOPROTECTANT CALCIUM ION (CA): FROM STORAGE BUFFER OF WATER AND 2MM CACL2 CELLOHEXAOSE (XYP): ONLY THREE OF THE XYP UNITS OF THE XYLOHEXAOSE ARE DEFINED.
Sequence detailsTHE PROTEIN SEQUENCE OF THE CONSTRUCT CORRESPONDS TO AMINO ACID RESIDUES 32 TO 551 WITH THE E337A ...THE PROTEIN SEQUENCE OF THE CONSTRUCT CORRESPONDS TO AMINO ACID RESIDUES 32 TO 551 WITH THE E337A MUTATION AND AN ADDITIONAL TWENTY AMINO ACID RESIDUES AT THE N-TERMINUS, MGSSHHHHHHSSGLVPRGSH. LINKER REGION BETWEEN AMINO ACID RESIDUES A182 TO A188 AND B182 AND B185 ARE NOT SEEN IN THE ELECTRON DENSITY MAPS.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growTemperature: 292 K / pH: 5.6
Details: 0.1 M NA CITRATE, PH 5.6, 1.0M (NH4)H2PO4 AT 292 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→101.1 Å / Num. obs: 81445 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXSOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→101.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 10.734 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 4129 5.1 %RANDOM
Rwork0.14677 ---
obs0.1489 77275 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.533 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0.71 Å20 Å2
2---1.41 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→101.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8086 0 140 934 9160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0228474
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.93611512
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42451052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16825.37432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.902151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2181534
X-RAY DIFFRACTIONr_chiral_restr0.1290.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026534
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0141.55139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90628280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.37433335
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0984.53218
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 309 -
Rwork0.298 5655 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.67512.6129-0.65644.78651.80312.74370.5238-1.21120.0069-0.4089-0.88380.5053-0.7053-0.26510.35990.83430.2978-0.26280.31120.04240.5832115.842966.883927.3428
21.9068-0.2731-0.09692.04670.37963.8899-0.0893-0.0989-0.36360.0875-0.08520.8865-0.5322-0.60760.17440.33760.251-0.13770.16910.03690.7592109.802660.899720.3052
32.8297-0.04750.38311.8274-2.36387.9556-0.4701-0.8164-0.49430.3070.24340.943-0.4742-1.2910.22670.18420.30620.20270.4076-0.01840.9997101.858561.230728.5509
44.4059-0.3031-2.21921.5787-0.65989.5859-0.4507-0.5428-0.50360.4796-0.1260.4062-0.963-0.05570.57670.33880.18610.02240.11810.09370.886111.479161.436329.0916
51.236-0.2520.361.5996-0.25741.4057-0.02320.2020.0727-0.3105-0.05050.1958-0.10180.01080.07370.26340.0398-0.05960.19730.07690.3037130.634145.227613.8641
61.0290.06160.30371.5278-0.24781.4373-0.0460.06530.22730.0596-0.0474-0.1326-0.25250.13210.09340.2164-0.0082-0.03620.19890.06620.3295144.375546.150928.7341
72.2121-0.3112-2.60393.0115-1.61316.07450.14230.59060.2452-0.53010.20460.39860.5893-1.2455-0.34680.1858-0.16860.04180.41190.09640.485797.818515.742435.4772
83.1911-0.4945-1.50162.31480.00854.31440.35780.01630.5588-0.00910.23690.0497-0.2724-0.5832-0.59470.0567-0.03710.14880.31120.07980.609697.068524.760742.0869
98.7145-0.6249-7.3292.21270.04279.90261.25421.11021.2632-0.47340.0685-0.0525-0.9994-1.6153-1.32270.17240.2230.28580.54910.52810.637391.103429.206733.2223
104.2643-1.2865-2.46422.6817-0.01746.04770.2098-0.00120.2842-0.24560.1011-0.64740.65370.4842-0.31090.25370.05940.13060.36660.02030.7692110.196817.667132.6222
111.06280.1233-0.0960.79960.1951.1120.0666-0.15740.05540.1072-0.10810.07290.0688-0.04760.04150.1962-0.03690.02310.1953-0.01480.2941127.811722.393546.8815
121.62620.309-0.77944.4134-0.40731.68950.02910.0019-0.065-0.0877-0.05350.17330.2959-0.27640.02440.2609-0.0226-0.0120.1936-0.04930.2775126.77686.358327.1659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 48
2X-RAY DIFFRACTION2A49 - 96
3X-RAY DIFFRACTION3A97 - 151
4X-RAY DIFFRACTION4A152 - 181
5X-RAY DIFFRACTION5A189 - 414
6X-RAY DIFFRACTION6A415 - 551
7X-RAY DIFFRACTION7B32 - 48
8X-RAY DIFFRACTION8B49 - 96
9X-RAY DIFFRACTION9B97 - 151
10X-RAY DIFFRACTION10B152 - 181
11X-RAY DIFFRACTION11B186 - 523
12X-RAY DIFFRACTION12B524 - 551

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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

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