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- PDB-6g21: Crystal structure of an esterase from Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 6g21
TitleCrystal structure of an esterase from Aspergillus oryzae
ComponentsProbable feruloyl esterase B-2
KeywordsHYDROLASE / esterase
Function / homology
Function and homology information


feruloyl esterase / feruloyl esterase activity / xylan catabolic process / extracellular region / metal ion binding
Similarity search - Function
Tannase/feruloyl esterase / Tannase and feruloyl esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Probable feruloyl esterase B-2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsMoroz, O.V. / Blagova, E. / Davies, G.J. / Wilson, K.S.
CitationJournal: To Be Published
Title: Crystal structure of an esterase from Aspergillus oryzae
Authors: Moroz, O.V. / Blagova, E. / Davies, G.J. / Wilson, K.S.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable feruloyl esterase B-2
B: Probable feruloyl esterase B-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,10920
Polymers111,7162
Non-polymers3,39318
Water7,855436
1
A: Probable feruloyl esterase B-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,81511
Polymers55,8581
Non-polymers1,95710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable feruloyl esterase B-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2949
Polymers55,8581
Non-polymers1,4368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.472, 119.472, 142.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 507
2010B4 - 507

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable feruloyl esterase B-2 / Ferulic acid esterase B-2 / FAEB-2


Mass: 55858.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold)
Strain: ATCC 42149 / RIB 40 / Gene: faeB-2, AO090001000582 / Production host: Aspergillus oryzae (mold) / References: UniProt: Q2UMX6, feruloyl esterase

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Sugars , 2 types, 11 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 443 molecules

#4: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID / Ferulic acid


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6353.31
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetailsDetails
2931vapor diffusion, sitting drop8.5ammonium sulphate, Tris buffer
2932vapor diffusion, sitting droplithium sulphate, tris buffer,CRYSTALS SOAKED IN 5mM KPTCL4CRYSTALS SOAKED IN 5mM KPTCL4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I04-110.92
SYNCHROTRONDiamond I0421.072
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELMay 28, 2012
DECTRIS PILATUS 6M-F2PIXELOct 21, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
21.0721
Reflection

Entry-ID: 6G21 / % possible obs: 100 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)CC1/2
2.1-37.726732618.524.80.099125.6
2.7-59.3735874411.40.09223.40.996
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.1-2.1519.20.744.845090.930.250.781100
2.7-2.7711.53.522990.8622

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
CRANKphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→37.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.811 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19429 3246 4.8 %RANDOM
Rwork0.15385 ---
obs0.15584 64050 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.84 Å2
Refinement stepCycle: 1 / Resolution: 2.1→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7777 0 213 436 8426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198235
X-RAY DIFFRACTIONr_bond_other_d0.0010.027071
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.96711238
X-RAY DIFFRACTIONr_angle_other_deg0.916316473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69551010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36824.483377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.281151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6711534
X-RAY DIFFRACTIONr_chiral_restr0.1070.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021724
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3292.9444040
X-RAY DIFFRACTIONr_mcbond_other2.3292.9444039
X-RAY DIFFRACTIONr_mcangle_it3.0834.3995050
X-RAY DIFFRACTIONr_mcangle_other3.0834.45051
X-RAY DIFFRACTIONr_scbond_it3.0143.2644195
X-RAY DIFFRACTIONr_scbond_other2.9823.2584184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3234.7996171
X-RAY DIFFRACTIONr_long_range_B_refined5.28735.4269406
X-RAY DIFFRACTIONr_long_range_B_other5.26335.3639349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16667 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 270 -
Rwork0.182 4681 -
obs--100 %

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