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

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Basic information

Entry
Database: PDB / ID: 6jca
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in I222 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: 2.1 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

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Assembly

Deposited unit
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,95710
Polymers114,4392
Non-polymers5188
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-126 kcal/mol
Surface area37540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.090, 125.220, 155.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / 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-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein CrmG


Mass: 57219.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoalloteichus sp. WH1-2216-6 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: H8Y6N2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG5000 MME, 100mM Tris pH 8.0 and 200mM Lithium sulfate

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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 S 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: 2.1→62.61 Å / Num. obs: 64955 / % possible obs: 99.2 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.055 / Rrim(I) all: 0.117 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.154.40.74645420.7380.3980.84899.9
9.62-62.614.30.0267510.9980.0140.0399.3

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Processing

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

5dds


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.654 / SU ML: 0.142 / SU R Cruickshank DPI: 0.2117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.178
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 3153 4.9 %RANDOM
Rwork0.1859 ---
obs0.1879 61786 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.44 Å2 / Biso mean: 31.5 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å2-0 Å20 Å2
2--1.02 Å2-0 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 26 330 8194
Biso mean--55.91 32.3 -
Num. residues----1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177542
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6410810
X-RAY DIFFRACTIONr_angle_other_deg1.3071.57617351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44551014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48620.385467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.728151327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9671589
X-RAY DIFFRACTIONr_chiral_restr0.0690.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021783
Refine LS restraints NCS

Ens-ID: 1 / Number: 14919 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 212 -
Rwork0.263 4526 -
all-4738 -
obs--99.75 %

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