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- PDB-6jc8: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

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Basic information

Entry
Database: PDB / ID: 6jc8
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Glu
ComponentsCrmG
KeywordsTRANSFERASE / aminotransferase / CrmG / Amino donor
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: 2.25 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
B: CrmG
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,56710
Polymers228,8784
Non-polymers1,6896
Water9,872548
1
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2845
Polymers114,4392
Non-polymers8453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-47 kcal/mol
Surface area36510 Å2
MethodPISA
2
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2845
Polymers114,4392
Non-polymers8453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-48 kcal/mol
Surface area36560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.090, 83.930, 88.459
Angle α, β, γ (deg.)106.600, 109.110, 95.130
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 6 - 522 / Label seq-ID: 6 - 522

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
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: Chemical
ChemComp-PL6 / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid


Mass: 376.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H17N2O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.42 Å3/Da / Density % sol: 49.15 % / Mosaicity: 0.48 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M Sodium acetate, 0.1M 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: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.25→49.46 Å / Num. obs: 96761 / % possible obs: 95 % / Redundancy: 3.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.071 / Rrim(I) all: 0.141 / Net I/σ(I): 8.6 / Num. measured all: 380457 / Scaling rejects: 145
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
2.25-2.293.90.6281898148220.7720.3680.7282.395.5
12.32-49.463.70.05822295990.9920.0350.06719.996.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DDS

5dds


Resolution: 2.25→49.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2049 / WRfactor Rwork: 0.1682 / FOM work R set: 0.8386 / SU B: 6.451 / SU ML: 0.153 / SU R Cruickshank DPI: 0.3274 / SU Rfree: 0.2114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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
Rfree0.2146 4706 4.9 %RANDOM
Rwork0.1769 ---
obs0.1788 92048 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.05 Å2 / Biso mean: 29.293 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.15 Å2-0.25 Å2
2---0.31 Å2-0.46 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 2.25→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15832 0 112 548 16492
Biso mean--36.95 26.15 -
Num. residues----2048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316210
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715288
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.64821962
X-RAY DIFFRACTIONr_angle_other_deg1.311.57935176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86452040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.32820.422948
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.447152696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.79215180
X-RAY DIFFRACTIONr_chiral_restr0.0730.22108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023608
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumber
11A16248
12B16248
21A16257
22C16257
31A16233
32D16233
41B16290
42C16290
51B16331
52D16331
61C16260
62D16260
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 335 -
Rwork0.259 6828 -
all-7163 -
obs--95.24 %

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