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- PDB-6jcb: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

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Basic information

Entry
Database: PDB / ID: 6jcb
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in C2 space group
ComponentsCrmG
KeywordsTRANSFERASE / aminotransferase / CrmG
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500638 China
CitationJournal: Commun Biol / Year: 2020
Title: Structural studies reveal flexible roof of active site responsible for omega-transaminase CrmG overcoming by-product inhibition.
Authors: Xu, J. / Tang, X. / Zhu, Y. / Yu, Z. / Su, K. / Zhang, Y. / Dong, Y. / Zhu, W. / Zhang, C. / Wu, R. / Liu, J.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CrmG
C: CrmG
B: CrmG
D: CrmG


Theoretical massNumber of molelcules
Total (without water)228,8784
Polymers228,8784
Non-polymers00
Water2,144119
1
A: CrmG
B: CrmG


Theoretical massNumber of molelcules
Total (without water)114,4392
Polymers114,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-26 kcal/mol
Surface area38510 Å2
MethodPISA
2
C: CrmG
D: CrmG


Theoretical massNumber of molelcules
Total (without water)114,4392
Polymers114,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-29 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.130, 114.830, 156.170
Angle α, β, γ (deg.)90.000, 92.160, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23D
14C
24B
15C
25D
16B
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 6 - 523 / Label seq-ID: 6 - 523

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22BC
13AA
23DD
14CB
24BC
15CB
25DD
16BC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
CrmG


Mass: 57219.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoalloteichus sp. WH1-2216-6 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H8Y6N2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.39 Å3/Da / Density % sol: 48.55 % / Mosaicity: 0.98 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M Sodium acetate, 0.1 M TRIS pH 8.5, 32%PEG 3350, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.85→38.87 Å / Num. obs: 47035 / % possible obs: 93.5 % / Redundancy: 2.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.086 / Rrim(I) all: 0.146 / Net I/σ(I): 6.1 / Num. measured all: 117939 / Scaling rejects: 180
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-2.942.60.4531137244320.8360.3290.5632.195.9
11.4-38.872.50.04817997260.9930.0370.0611488.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DDS

5dds


Resolution: 2.85→18 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2476 / WRfactor Rwork: 0.1939 / FOM work R set: 0.7271 / SU B: 18.531 / SU ML: 0.345 / SU Rfree: 0.4538 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 2330 5 %RANDOM
Rwork0.2101 ---
obs0.2126 44504 92.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.77 Å2 / Biso mean: 36.894 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.92 Å2
2---0.47 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 2.85→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15021 0 0 119 15140
Biso mean---17.99 -
Num. residues----1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01315257
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714457
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6420639
X-RAY DIFFRACTIONr_angle_other_deg1.2221.57633237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58451929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48320.329911
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.202152561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.30315176
X-RAY DIFFRACTIONr_chiral_restr0.0620.21988
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023427
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A15028
12C15028
21A14983
22B14983
31A15006
32D15006
41C14971
42B14971
51C15045
52D15045
61B14960
62D14960
LS refinement shellResolution: 2.85→2.922 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 166 -
Rwork0.306 3300 -
all-3466 -
obs--95.59 %

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