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- PDB-3jug: Crystal structure of endo-beta-1,4-mannanase from the alkaliphili... -

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Basic information

Entry
Database: PDB / ID: 3jug
TitleCrystal structure of endo-beta-1,4-mannanase from the alkaliphilic Bacillus sp. N16-5
ComponentsBeta-mannanase
KeywordsHYDROLASE / TIM-BARREL / Glycosidase
Function / homology
Function and homology information


beta-mannosidase activity / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / organic substance metabolic process / membrane
Similarity search - Function
: / Mannanase, galactose-binding domain-like / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus (Bacillus rRNA group 1)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhao, Y. / Zhang, Y. / Xue, Y.
CitationJournal: To be Published
Title: Structure Analysis of Alkaline beta-mannanase from Alkaliphilic Bacillus sp. N16-5 Implications for Adaptation to Alkaline Conditions
Authors: Zhao, Y. / Zhang, Y. / Cao, Y. / Qi, J. / Xue, Y. / Gao, F. / Peng, H. / Gao, G.F. / Ma, Y.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2652
Polymers38,1691
Non-polymers961
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.033, 63.312, 83.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-mannanase


Mass: 38168.770 Da / Num. of mol.: 1 / Fragment: endo-beta-mannanase, UNP residues 32-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Strain: N16-5 / Gene: manA / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5YEX6, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

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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: 39.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M Ammonium Sulphate, 0.1M sodium citrate, 1.2M Lithium Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→63.29 Å / Num. obs: 38945 / % possible obs: 92.74 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.68 % / Biso Wilson estimate: 6.94 Å2 / Rsym value: 0.0764
Reflection shellResolution: 1.6→1.71 Å / Redundancy: 1.54 % / Num. unique all: 4841 / % possible all: 65.44

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WKY

1wky


Resolution: 1.6→43.176 Å / FOM work R set: 0.86 / SU ML: 0.19 / σ(F): 0.13 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1835 5.13 %random
Rwork0.1737 ---
all0.1758 35784 --
obs0.1758 35784 84.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.519 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 12.388 Å2
Baniso -1Baniso -2Baniso -3
1-1.355 Å2-0 Å2-0 Å2
2---0.691 Å20 Å2
3----2.483 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 5 589 2894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072375
X-RAY DIFFRACTIONf_angle_d1.113244
X-RAY DIFFRACTIONf_dihedral_angle_d15.228800
X-RAY DIFFRACTIONf_chiral_restr0.08343
X-RAY DIFFRACTIONf_plane_restr0.004426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5967-1.63980.3351520.3195917X-RAY DIFFRACTION30
1.6398-1.68810.3251860.28311767X-RAY DIFFRACTION58
1.6881-1.74260.31221360.24082309X-RAY DIFFRACTION76
1.7426-1.80490.25611230.19112536X-RAY DIFFRACTION83
1.8049-1.87710.2191480.15432692X-RAY DIFFRACTION89
1.8771-1.96260.17151540.13042796X-RAY DIFFRACTION92
1.9626-2.0660.16251640.13452850X-RAY DIFFRACTION94
2.066-2.19550.16451410.14322939X-RAY DIFFRACTION95
2.1955-2.3650.20991590.15532913X-RAY DIFFRACTION95
2.365-2.60290.21211600.15962995X-RAY DIFFRACTION97
2.6029-2.97950.21751690.17313030X-RAY DIFFRACTION97
2.9795-3.75350.1881720.16653043X-RAY DIFFRACTION97
3.7535-43.1920.22271710.1883162X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 17.1848 Å / Origin y: -1.5875 Å / Origin z: -11.9158 Å
111213212223313233
T0.0043 Å2-0.001 Å2-0.0003 Å2-0.0045 Å20.0035 Å2--0.005 Å2
L0.1076 °2-0.0077 °20.027 °2-0.1541 °2-0.0884 °2--0.2615 °2
S-0.0187 Å °0.0069 Å °0.0135 Å °0.0078 Å °0.0082 Å °0.0013 Å °-0.0037 Å °-0.0258 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA34 - 329
2X-RAY DIFFRACTION1allA1
3X-RAY DIFFRACTION1all1 - 589

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