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- PDB-1zmb: Crystal Structure of the Putative Acetylxylan Esterase from Clost... -

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Basic information

Entry
Database: PDB / ID: 1zmb
TitleCrystal Structure of the Putative Acetylxylan Esterase from Clostridium acetobutylicum, Northeast Structural Genomics Target CaR6
ComponentsAcetylxylan esterase related enzyme
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #10 / : / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase / SGNH hydrolase superfamily / Helix non-globular / Special / Rossmann fold ...Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #10 / : / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase / SGNH hydrolase superfamily / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylxylan esterase related enzyme
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsForouhar, F. / Vorobiev, S.M. / Abashidze, M. / Ciao, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative Acetylxylan Esterase from Clostridium acetobutylicum, Northeast Structural Genomics Target CaR6
Authors: Forouhar, F. / Vorobiev, S.M. / Abashidze, M. / Ciao, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylxylan esterase related enzyme
B: Acetylxylan esterase related enzyme
C: Acetylxylan esterase related enzyme
D: Acetylxylan esterase related enzyme
E: Acetylxylan esterase related enzyme
F: Acetylxylan esterase related enzyme


Theoretical massNumber of molelcules
Total (without water)202,3256
Polymers202,3256
Non-polymers00
Water2,216123
1
A: Acetylxylan esterase related enzyme
B: Acetylxylan esterase related enzyme


Theoretical massNumber of molelcules
Total (without water)67,4422
Polymers67,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-22 kcal/mol
Surface area22700 Å2
MethodPISA
2
C: Acetylxylan esterase related enzyme
D: Acetylxylan esterase related enzyme


Theoretical massNumber of molelcules
Total (without water)67,4422
Polymers67,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area22640 Å2
MethodPISA
3
E: Acetylxylan esterase related enzyme
F: Acetylxylan esterase related enzyme


Theoretical massNumber of molelcules
Total (without water)67,4422
Polymers67,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-23 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.999, 87.936, 103.510
Angle α, β, γ (deg.)106.50, 100.22, 113.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Acetylxylan esterase related enzyme


Mass: 33720.801 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Plasmid: pET21(BL21) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q97LM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 10% PEG 20K, and 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 124903 / Num. obs: 118658 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.076 / Net I/σ(I): 14.04
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3 / Num. unique all: 11527 / Rsym value: 0.341 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.61→29.31 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 243470.2 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 10170 9.7 %RANDOM
Rwork0.243 ---
all0.245 118658 --
obs0.243 104393 82.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.2867 Å2 / ksol: 0.316861 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å23.94 Å21.7 Å2
2---1.07 Å26.87 Å2
3---0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.61→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13668 0 0 123 13791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 1090 9.3 %
Rwork0.304 10598 -
obs-10598 55.1 %

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