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- PDB-6k52: Hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microb... -

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Basic information

Entry
Database: PDB / ID: 6k52
TitleHyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microbial flora of a Japanese hot spring
ComponentsGH6 cellobiohydrolase, HMCEL6A
KeywordsHYDROLASE / glycoside hydrolase / GH6 / thermostable
Function / homology1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ACETATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68000139531 Å
AuthorsBaba, S. / Takeda, M. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T.
CitationJournal: To Be Published
Title: A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data
Authors: Takeda, M. / Baba, S. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 23, 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: GH6 cellobiohydrolase, HMCEL6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0785
Polymers46,8981
Non-polymers1794
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.168, 141.168, 223.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-974-

HOH

21A-1180-

HOH

31A-1186-

HOH

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Components

#1: Protein GH6 cellobiohydrolase, HMCEL6A


Mass: 46898.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
References: cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A LOCUS/ACCESSION NUMBER OF LC163905.

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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: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (W/V) PEG 1000, 0.2M CAICIUM ACETATE, 0.1M IMIDAZOLE (PH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 97033 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 17.3900593193 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.018 / Rrim(I) all: 0.074 / Net I/σ(I): 36.7
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 9626 / CC1/2: 0.961 / Rpim(I) all: 0.155 / Rrim(I) all: 0.617 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OC5

1oc5


Resolution: 1.68000139531→32.9103974351 Å / SU ML: 0.176042297081 / Cross valid method: FREE R-VALUE / σ(F): 1.33476296841 / Phase error: 21.1813420271
RfactorNum. reflection% reflection
Rfree0.195841394201 4840 5.0440836234 %
Rwork0.174638367187 --
obs0.1756834674 95954 98.86457303 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.3657637173 Å2
Refinement stepCycle: LAST / Resolution: 1.68000139531→32.9103974351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 7 589 3905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007221098295143555
X-RAY DIFFRACTIONf_angle_d1.12721609134897
X-RAY DIFFRACTIONf_chiral_restr0.0777181036092520
X-RAY DIFFRACTIONf_plane_restr0.00506323400149670
X-RAY DIFFRACTIONf_dihedral_angle_d21.08293570611340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69910.2655220208571540.2376540680663044X-RAY DIFFRACTION99.4712286159
1.6991-1.71910.2845406497761720.2426936830762984X-RAY DIFFRACTION99.5897759546
1.7191-1.740.2507557480191590.234608210163023X-RAY DIFFRACTION99.4685839325
1.74-1.76210.2932724034351630.2358931710413054X-RAY DIFFRACTION99.1676942047
1.7621-1.78530.26809826621510.2324209095623028X-RAY DIFFRACTION99.2816989382
1.7853-1.80970.2801668138021740.2361823602473043X-RAY DIFFRACTION99.1371340524
1.8097-1.83560.2771355571831620.2343458506352994X-RAY DIFFRACTION98.779342723
1.8356-1.8630.2575823937661480.2338851444292958X-RAY DIFFRACTION97.888433659
1.863-1.89210.2298249690621570.2124631598163011X-RAY DIFFRACTION98.1108702385
1.8921-1.92310.2291705156551530.2128091512082986X-RAY DIFFRACTION98.2165206508
1.9231-1.95620.2276554628851490.2083759358423053X-RAY DIFFRACTION98.4927714549
1.9562-1.99180.2281554799691730.1978566068513023X-RAY DIFFRACTION99.4090202177
1.9918-2.03010.2365971447991660.1941375788543038X-RAY DIFFRACTION99.7198879552
2.0301-2.07150.2173211887061730.1837126161943063X-RAY DIFFRACTION99.8765432099
2.0715-2.11660.2033242466231510.1852578297183030X-RAY DIFFRACTION99.5618153365
2.1166-2.16580.2116982073051560.1821532432593070X-RAY DIFFRACTION99.4144838213
2.1658-2.220.2132421013271520.1835984926123021X-RAY DIFFRACTION99.063378083
2.22-2.280.2142476467141660.1829746182933014X-RAY DIFFRACTION98.4215413185
2.28-2.3470.1794054679411450.1780296583563039X-RAY DIFFRACTION98.5148514851
2.347-2.42280.189164419671690.1781981112442978X-RAY DIFFRACTION97.3098330241
2.4228-2.50930.2185632410871820.1705370794552971X-RAY DIFFRACTION97.5858867224
2.5093-2.60980.2002726119651620.1776128838523001X-RAY DIFFRACTION97.9863692689
2.6098-2.72850.2234576693631840.1790137696522980X-RAY DIFFRACTION97.6543209877
2.7285-2.87230.1870460706871550.1789178251263025X-RAY DIFFRACTION97.9064039409
2.8723-3.05210.2104444945321610.1798056309833021X-RAY DIFFRACTION98.1795742055
3.0521-3.28750.1964934573061390.1718583262123104X-RAY DIFFRACTION99.4175352544
3.2875-3.6180.1459570514961690.1477670695393109X-RAY DIFFRACTION99.9085644621
3.618-4.14070.1339618580551540.1362989881323119X-RAY DIFFRACTION99.7257769653
4.1407-5.21350.1475090373621850.1304170389963099X-RAY DIFFRACTION99.5755003032
5.2135-32.91670.1822440340121560.1585616514433231X-RAY DIFFRACTION99.0930368637

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