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

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Basic information

Entry
Database: PDB / ID: 3civ
TitleCrystal structure of the endo-beta-1,4-mannanase from Alicyclobacillus acidocaldarius
ComponentsEndo-beta-1,4-mannanase
KeywordsHYDROLASE / TIM BARREL
Function / homologyGlycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Endo-beta-1,4-mannanase
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsMa, Y. / Zhang, Y. / Xue, Y.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A
Authors: Zhang, Y. / Ju, J. / Peng, H. / Gao, F. / Zhou, C. / Zeng, Y. / Xue, Y. / Li, Y. / Henrissat, B. / Gao, G.F. / Ma, Y.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray study of native and selenomethionyl beta-1,4-mannanase AaManA from Alicyclobacillus acidocaldarius Tc-12-31
Authors: Zhang, Y. / Gao, F. / Xue, Y. / Zeng, Y. / Peng, H. / Qi, J. / Ma, Y.
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-beta-1,4-mannanase


Theoretical massNumber of molelcules
Total (without water)38,8041
Polymers38,8041
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.338, 75.554, 88.016
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 Endo-beta-1,4-mannanase


Mass: 38803.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Strain: Tc-12-31 / Gene: AamanA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5H1I6, mannan endo-1,4-beta-mannosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium dihydrogen phosphate, 0.1M sodium citrate (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 VII / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35.07 Å / Num. obs: 23386 / % possible obs: 97.3 % / Redundancy: 6.92 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 10.2 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.86 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21208 1206 5.2 %RANDOM
Rwork0.1737 ---
obs0.17571 22180 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.037 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 0 221 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212605
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.9213541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57522.595131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.611522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022082
X-RAY DIFFRACTIONr_nbd_refined0.1820.21314
X-RAY DIFFRACTIONr_nbtor_refined0.30.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.220
X-RAY DIFFRACTIONr_mcbond_it0.5771.51623
X-RAY DIFFRACTIONr_mcangle_it0.92122511
X-RAY DIFFRACTIONr_scbond_it1.41831181
X-RAY DIFFRACTIONr_scangle_it2.2824.51030
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 84 -
Rwork0.205 1435 -
obs--86.75 %

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