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- PDB-6r2j: Crystal Structure of Pseudomonas stutzeri endoglucanase Cel5A in ... -

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Basic information

Entry
Database: PDB / ID: 6r2j
TitleCrystal Structure of Pseudomonas stutzeri endoglucanase Cel5A in complex with cellobiose
ComponentsEndoglucanase(Endo-1,4-beta-glucanase)protein
KeywordsHYDROLASE / Cellulase / endoglucanase / GH5 / transglycosylation / cellobiose
Function / homology
Function and homology information


glucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / Endoglucanase(Endo-1,4-beta-glucanase)protein
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsDutoit, R. / Delsaute, M. / Berlemont, R. / Van Elder, D. / Galleni, M. / Bauvois, C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes.
Authors: Dutoit, R. / Delsaute, M. / Collet, L. / Vander Wauven, C. / Van Elder, D. / Berlemont, R. / Richel, A. / Galleni, M. / Bauvois, C.
History
DepositionMar 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase(Endo-1,4-beta-glucanase)protein
B: Endoglucanase(Endo-1,4-beta-glucanase)protein
C: Endoglucanase(Endo-1,4-beta-glucanase)protein
D: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,04110
Polymers148,8674
Non-polymers1,1736
Water34,9491940
1
A: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6813
Polymers37,2171
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3392
Polymers37,2171
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3392
Polymers37,2171
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase(Endo-1,4-beta-glucanase)protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6813
Polymers37,2171
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.250, 82.820, 104.680
Angle α, β, γ (deg.)90.000, 91.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoglucanase(Endo-1,4-beta-glucanase)protein


Mass: 37216.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (strain A1501) (bacteria)
Gene: PST_2494 / Plasmid: pET22b-Cel5 / Details (production host): pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4VME5
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1940 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ps_Cel5A (27 microM) in 50 mM sodium phosphate pH 7.0, was mixed 1:1 with 100 mM tris pH 5.9 22.5 % PEG600 0.1 % cellobiose. The crystal was soaked 1 hour in 100 mM Tris pH 5.9 30% PEG600.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.14
ReflectionResolution: 1.44→48.19 Å / Num. obs: 216633 / % possible obs: 99.1 % / Redundancy: 6.753 % / Biso Wilson estimate: 18.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 0.981 / Net I/σ(I): 19.06 / Num. measured all: 1462858 / Scaling rejects: 224
Reflection shellResolution: 1.44→48.19 Å / Redundancy: 5.97 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 5.11 / Num. measured obs: 16755 / Num. possible: 2543 / Num. unique obs: 2482 / CC1/2: 0.998 / Rrim(I) all: 0.04 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.89 Å48.19 Å
Translation1.89 Å48.19 Å

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Processing

Software
NameVersionClassification
PHENIXV.1.14-3260refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LX4

4lx4


Resolution: 1.44→48.19 Å / Cross valid method: THROUGHOUT / σ(F): 2.42 / Phase error: 24.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.224 11122 5.13 %
Rwork0.179 205789 -
obs0.181 216633 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 15.92 Å2 / Biso min: 3.27 Å2
Refinement stepCycle: final / Resolution: 1.44→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10432 0 145 1940 12517
Biso mean--31.14 26.49 -
Num. residues----1310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.45990.2575210.225598821040391
1.4599-1.48640.27335350.2405101741070993
1.4864-1.5150.26645330.2249101171065094
1.515-1.54590.25325360.2173101941073094
1.5459-1.57960.26045400.2141102621080294
1.5796-1.61630.24175370.2112102001073794
1.6163-1.65670.25465400.2089102611080194
1.6567-1.70150.24275390.2094102321077194
1.7015-1.75160.24455440.2039103421088694
1.7516-1.80810.23335400.2044102591079994
1.8081-1.87280.22765440.2006103291087395
1.8728-1.94770.27075400.2265102621080294
1.9477-2.03640.22625440.1894103471089195
2.0364-2.14380.22375460.1804103801092695
2.1438-2.27810.24725460.1968103691091595
2.2781-2.45390.215460.1701103641091095
2.4539-2.70090.20515480.169104271097595
2.7009-3.09160.20635480.1545104001094895
3.0916-3.89480.19865510.1396104641101595
3.8948-47.1980.19385540.1446105241107894
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)
12.9484-0.9274-1.33121.47760.49371.7037-0.005-0.0124-0.12820.021-0.0520.16850.008-0.08340.04640.0473-0.0229-0.01690.0465-0.01590.0702-4.5235-5.3036-47.0747
21.41140.3052-0.21261.12120.34440.76570.01020.0853-0.1154-0.054-0.05180.09590.0612-0.060.02490.06570.0006-0.01850.0565-0.00320.0774-1.7303-9.9235-54.4741
30.99580.2373-0.05291.2180.12940.71350.01180.07150.0785-0.1038-0.01430.0246-0.0569-0.0044-0.00690.06340.00260.00250.05540.00660.06984.79535.105-52.3822
40.6614-0.30660.72383.2249-2.67223.037-0.0111-0.10540.08010.1126-0.0064-0.0311-0.1405-0.08330.0390.07220.00170.01870.0733-0.01890.07963.09326.2782-40.2251
51.0375-0.60560.19842.4248-0.60091.28970.0226-0.20970.10950.2927-0.02830.0447-0.12450.04240.02850.099-0.03110.03540.1207-0.0270.0958-1.91462.8198-30.7055
61.2873-0.4481-0.0261.0323-0.04521.2350.0102-0.1298-0.0340.0266-0.01290.18580.101-0.0797-0.00120.0651-0.02770.02030.08360.00130.1094-7.4877-7.3397-36.7616
72.6313-1.0793-0.93081.62450.54551.3892-0.01220.0446-0.0845-0.0263-0.00470.08040.0367-0.10660.01580.054-0.0312-0.00210.0466-0.00580.0615-2.1694-10.0998-98.7223
83.2196-0.7444-1.93710.91830.44751.5803-0.09690.0683-0.35240.0523-0.00190.01750.1378-0.1320.07240.0812-0.0253-0.00150.0498-0.00220.1143-1.6509-20.4882-100.4332
92.14670.1238-1.19311.1484-0.04371.8242-0.02950.2619-0.0005-0.09960.0357-0.08530.0191-0.1065-0.01530.0556-0.0090.00250.0551-0.00880.06066.1227-9.046-107.8023
106.0237-0.4167-3.59791.08870.55773.0721-0.06080.1899-0.1133-0.08560.01990.00580.1499-0.12320.06470.0802-0.018-0.01760.0685-0.01110.0693-2.8182-15.2564-110.4233
111.41830.314-0.14951.221-0.19010.8155-0.02950.154-0.0181-0.14380.0261-0.0915-0.04470.06750.00860.063-0.0060.01470.0566-0.00960.06587.5088-1.5065-106.7833
120.53770.0727-0.1061.0387-0.72831.8533-0.0014-0.08390.06820.1013-0.0416-0.0555-0.11310.09820.02670.0544-0.0087-0.00120.0678-0.02010.08794.23043.7552-92.3584
131.10970.0273-0.26161.75510.29241.2084-0.0091-0.162-0.0470.17880.01570.01520.0580.0495-0.02410.0532-0.00160.00650.07370.0050.0549-1.1675-7.4579-85.7999
141.30980.0317-0.20942.32040.71531.540.0031-0.3165-0.34050.1245-0.00620.04540.2944-0.01310.04380.1086-0.00710.02450.1010.03670.1103-4.0084-18.252-85.5909
150.7033-0.37210.06741.26090.52181.02920.0829-0.01870.3773-0.14640.02440.42-0.2292-0.06210.01320.10660.02570.0410.1079-0.00840.2261-12.21519.1105-89.9406
161.5901-0.2710.49280.8874-0.17641.4680.10560.11170.1772-0.1001-0.0621-0.0603-0.17220.0371-0.01540.11660.00770.05220.05120.01090.1012-28.2441-11.5841-77.4675
170.8237-0.3293-0.01811.06560.36711.38450.0250.1259-0.0756-0.1206-0.03070.0731-0.0101-0.138-0.00190.0707-0.00410.00250.0669-0.0070.0725-34.3761-26.0104-78.8933
180.379-0.281-0.72670.87360.85651.9326-0.01580.0265-0.10750.0241-0.0220.07460.0883-0.10770.07080.077-0.0021-0.00240.05940.00620.0855-34.5634-27.0799-66.4297
191.204-1.3456-0.76732.89351.77862.6412-0.1075-0.1569-0.22970.21940.01660.17030.1988-0.04930.06370.087-0.00240.02780.07350.03410.1221-34.9789-25.7383-54.3754
201.1038-0.3947-0.13232.57040.53091.3560.0166-0.1391-0.03990.04610.0575-0.01940.0113-0.0591-0.02290.0619-0.01030.01360.04120.00810.056-31.0137-20.7502-61.8215
211.3475-0.327-0.02210.4903-0.13641.15510.0571-0.17760.1432-0.01770.0483-0.076-0.22190.0867-0.04560.1013-0.02790.02570.0843-0.03540.079-26.4011-13.9914-59.3562
223.12750.85541.77020.90390.38761.77570.0121-0.153-0.007-0.0499-0.02250.1198-0.0332-0.176-0.03060.05110.03320.00740.07010.00610.1061-37.896326.4191-83.2056
231.34760.02670.32470.9190.48260.91610.0011-0.09630.10220.0055-0.04870.1165-0.1063-0.13710.0330.06840.01380.01710.0656-0.00560.0726-33.068330.5849-77.0977
246.3697-0.40242.89790.7546-0.68511.66750.0245-0.28530.25040.1281-0.13510.2449-0.2828-0.28730.07980.10130.04040.0370.1453-0.03870.1149-38.511430.9405-70.9963
251.9021-0.20610.28191.4757-0.09081.5510.0197-0.1143-0.08070.1969-0.0303-0.05720.1322-0.01080.01670.09780.0074-0.00140.06260.00350.0564-28.283617.8966-75.4441
260.68170.02870.19831.7881-0.17931.63040.04540.064-0.0798-0.0981-0.0195-0.00140.11360.0362-0.01480.07010.0103-0.00260.0534-0.01020.0911-30.851313.3329-90.5231
271.1299-0.17940.36691.27320.02261.4059-0.01190.12130.0582-0.2954-0.00560.1406-0.0978-0.019-0.01360.10340.0153-0.02360.0620.00540.0677-36.367124.6949-96.0634
281.31150.2588-0.02462.04790.33461.0118-0.05230.21670.3202-0.0670.01670.1761-0.3204-0.14290.03330.18270.0382-0.05020.10090.02250.1498-39.617835.712-95.9346
291.2940.2835-0.22480.50950.88711.99840.02570.0567-0.3333-0.01330.0550.54330.3966-0.182-0.01650.1362-0.0531-0.08960.11710.01330.2674-47.71369.363-93.2505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )A1 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 90 )A32 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 188 )A91 - 188
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 218 )A189 - 218
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 276 )A219 - 276
6X-RAY DIFFRACTION6chain 'A' and (resid 277 through 326 )A277 - 326
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 31 )B1 - 31
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 50 )B32 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 73 )B51 - 73
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 90 )B74 - 90
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 151 )B91 - 151
12X-RAY DIFFRACTION12chain 'B' and (resid 152 through 244 )B152 - 244
13X-RAY DIFFRACTION13chain 'B' and (resid 245 through 292 )B245 - 292
14X-RAY DIFFRACTION14chain 'B' and (resid 293 through 313 )B293 - 313
15X-RAY DIFFRACTION15chain 'B' and (resid 314 through 330 )B314 - 330
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 90 )C1 - 90
17X-RAY DIFFRACTION17chain 'C' and (resid 91 through 188 )C91 - 188
18X-RAY DIFFRACTION18chain 'C' and (resid 189 through 218 )C189 - 218
19X-RAY DIFFRACTION19chain 'C' and (resid 219 through 243 )C219 - 243
20X-RAY DIFFRACTION20chain 'C' and (resid 244 through 259 )C244 - 259
21X-RAY DIFFRACTION21chain 'C' and (resid 260 through 325 )C260 - 325
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 31 )D1 - 31
23X-RAY DIFFRACTION23chain 'D' and (resid 32 through 73 )D32 - 73
24X-RAY DIFFRACTION24chain 'D' and (resid 74 through 90 )D74 - 90
25X-RAY DIFFRACTION25chain 'D' and (resid 91 through 151 )D91 - 151
26X-RAY DIFFRACTION26chain 'D' and (resid 152 through 244 )D152 - 244
27X-RAY DIFFRACTION27chain 'D' and (resid 245 through 292 )D245 - 292
28X-RAY DIFFRACTION28chain 'D' and (resid 293 through 313 )D293 - 313
29X-RAY DIFFRACTION29chain 'D' and (resid 314 through 329 )D314 - 329

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  • 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

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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

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