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- PDB-6pz7: GH5-4 broad specificity endoglucanase from Clostridium acetobutylicum -

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Basic information

Entry
Database: PDB / ID: 6pz7
TitleGH5-4 broad specificity endoglucanase from Clostridium acetobutylicum
ComponentsEndoglucanase family 5
KeywordsHYDROLASE / GH5-4 / endoglucanase / GLBRC
Function / homologyGlycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / Endoglucanase family 5
Function and homology information
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Fox, B.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-07ER64494 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis.
Authors: Glasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Structure summary / Category: pdbx_database_related / struct / Item: _struct.title
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5235
Polymers37,3021
Non-polymers2224
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.721, 51.965, 102.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endoglucanase family 5


Mass: 37301.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: CA_C0826 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q97KU0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein was crystallized in SD2 plates set by a Mosquito crystallization robot. The hit came from PACT Premiere Screen A7, 200 mM NaCl, 100 mM sodium acetate pH 5.0, 25% PEG 6K. Crystals ...Details: Protein was crystallized in SD2 plates set by a Mosquito crystallization robot. The hit came from PACT Premiere Screen A7, 200 mM NaCl, 100 mM sodium acetate pH 5.0, 25% PEG 6K. Crystals were cryopreserved in reservoir solution supplemented with 15% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.25→28.65 Å / Num. obs: 78485 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 9.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0649 / Rpim(I) all: 0.02472 / Rrim(I) all: 0.06959 / Net I/σ(I): 19.11
Reflection shellResolution: 1.25→1.295 Å / Rmerge(I) obs: 0.2093 / Mean I/σ(I) obs: 4.41 / Num. unique obs: 5788 / CC1/2: 0.955 / Rpim(I) all: 0.1166 / Rrim(I) all: 0.2412

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Processing

Software
NameVersionClassification
XDS20190315data reduction
XSCALE20190315data scaling
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDZ

3ndz


Resolution: 1.25→28.64 Å / SU ML: 0.0827 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.8069
RfactorNum. reflection% reflectionSelection details
Rfree0.1482 2449 3.27 %random selection
Rwork0.1255 ---
obs0.1262 74833 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.45 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 13 378 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042828
X-RAY DIFFRACTIONf_angle_d1.12533877
X-RAY DIFFRACTIONf_chiral_restr0.0876425
X-RAY DIFFRACTIONf_plane_restr0.0095506
X-RAY DIFFRACTIONf_dihedral_angle_d12.65511063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.20461040.17643167X-RAY DIFFRACTION72.96
1.28-1.30.18871210.15743586X-RAY DIFFRACTION81.69
1.3-1.330.16811390.14824057X-RAY DIFFRACTION93.27
1.33-1.370.14341430.13564262X-RAY DIFFRACTION97.87
1.37-1.40.14011490.13144318X-RAY DIFFRACTION98.96
1.4-1.450.14971470.12384323X-RAY DIFFRACTION99.11
1.45-1.490.16131440.12024343X-RAY DIFFRACTION99.36
1.49-1.550.12591420.11674339X-RAY DIFFRACTION99.45
1.55-1.610.14731500.1174364X-RAY DIFFRACTION99.62
1.61-1.680.1431470.11254376X-RAY DIFFRACTION99.47
1.68-1.770.12811480.1144359X-RAY DIFFRACTION99.84
1.77-1.880.12361490.11574414X-RAY DIFFRACTION99.82
1.88-2.020.14171480.11684417X-RAY DIFFRACTION99.93
2.02-2.230.1371490.11264439X-RAY DIFFRACTION100
2.23-2.550.13291550.11634440X-RAY DIFFRACTION99.96
2.55-3.210.15231540.13164525X-RAY DIFFRACTION99.94
3.21-28.640.16941600.13694655X-RAY DIFFRACTION99.44
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)
10.6809892368740.1451378134110.1082667718790.6081766872310.04811235270340.6721612748630.02199888440840.139973465680.00197723042808-0.152371515846-0.0877689864861-0.0452379706507-0.0589643382057-0.0182199230076-0.1569120839340.05457535924530.01887033872650.006613740157920.06970033979930.005825999095960.0371337750772-14.3984504122-2.069303337227.36096786379
20.246296052520.135515549883-0.02128848626250.278292994694-0.1748303255510.537845453257-0.02151054384770.0606316040710.09078980070960.0184660932438-0.0397621929778-0.0853081387334-0.063307924120.0519803362630.03929069231940.0616236504651-0.000488910619108-0.005474948998490.06116953171290.01389677087240.068268435392-16.37450831359.3351375678710.9233927122
30.492480233030.0800702222437-0.01532758895360.44299209169-0.1343581688120.364663072705-0.02414266463440.07549822667260.0861269528437-0.01711855549040.02705236740.00245832924009-0.0398287923866-0.0137495964443-0.3876902635760.06688334249450.00671311842335-0.00104853835460.05794662659710.0154256378260.0601170374606-21.36579233516.882679348318.13966860218
40.5793267560180.117119193336-0.1182168679980.416830158071-0.1349669128670.430959879938-0.01044918600370.09564113429790.0181286076206-0.02576609741430.05407824577670.03429500479640.0203404679882-0.0558455518388-0.02061639687440.060197024636-0.00314229669001-0.001030893941560.07336466510070.007225557830860.0553278595763-29.7369671341-1.791394806737.29376677134
50.577660741714-0.07749358699120.00991510430930.516408391084-0.4882994562880.3417908985130.0167716828396-0.0146527232363-0.1481473041850.00630729279542-0.0186879663082-0.0228005962970.08047899418570.0197823760612-0.02769480148560.07901525771680.00172903624464-0.0001818639874080.0552167508420.006373889716950.0857998854511-16.4196942354-13.398263170119.2792320806
60.09551165758460.01582821170630.041910316580.10981966986-0.007032550023270.2664718346180.05313549464210.0060758453621-0.1643036159230.0547825770165-0.0177174935974-0.1895332108490.1044205142480.121935255817-0.1647877054360.09184423297930.0144706027539-0.009363182627040.07558151609530.009048163757330.124621377063-7.19013113972-14.703385365418.1510743028
70.428133857577-0.1341733180110.2995810120660.47787242288-0.2810497574090.349499274917-0.01743518461470.01077978418460.01689521901180.106527371645-0.0360075978123-0.16811083391-0.01826306450.10401321677-0.03152843288170.0791076960993-0.00444752523322-0.01319663357950.08593132273550.01489822172020.0997137661048-5.96732248486-1.1442484613120.0590342833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 113 )
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 277 )
6X-RAY DIFFRACTION6chain 'A' and (resid 278 through 295 )
7X-RAY DIFFRACTION7chain 'A' and (resid 296 through 335 )

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