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- PDB-6jc9: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

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Basic information

Entry
Database: PDB / ID: 6jc9
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Gln
ComponentsCrmG
KeywordsTRANSFERASE / aminotransferase / CrmG / complex
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate 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
ACETIC ACID / GLUTAMINE / PYRIDOXAL-5'-PHOSPHATE / CrmG
Similarity search - Component
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,16511
Polymers228,8784
Non-polymers1,2877
Water7,440413
1
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9935
Polymers114,4392
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-47 kcal/mol
Surface area36960 Å2
MethodPISA
2
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1726
Polymers114,4392
Non-polymers7334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-48 kcal/mol
Surface area36440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.039, 83.879, 88.410
Angle α, β, γ (deg.)106.480, 109.170, 94.980
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: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / 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

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 420 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 49.11 % / Mosaicity: 0.76 °
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: BL17U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.35→50.59 Å / Num. obs: 81461 / % possible obs: 91.2 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.061 / Rrim(I) all: 0.113 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.393.20.49334610.750.3170.58972.4
12.44-50.583.10.0525560.9860.0360.06393

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5dds


Resolution: 2.35→50.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.009 / SU ML: 0.162 / SU R Cruickshank DPI: 0.4874 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.487 / ESU R Free: 0.234
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
Rfree0.2075 3991 4.9 %RANDOM
Rwork0.1717 ---
obs0.1734 77461 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.08 Å2 / Biso mean: 33.385 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20.18 Å2-0 Å2
2---0.5 Å2-0.63 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 2.35→50.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15804 0 80 413 16297
Biso mean--37.8 28.34 -
Num. residues----2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01316151
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715239
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6421876
X-RAY DIFFRACTIONr_angle_other_deg1.2791.57435053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68452034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.61920.422948
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.392152692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.40815180
X-RAY DIFFRACTIONr_chiral_restr0.0690.22101
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023594
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16209
12B16209
21A16241
22C16241
31A16087
32D16087
41B16295
42C16295
51B16103
52D16103
61C16076
62D16076
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 233 -
Rwork0.229 4772 -
all-5005 -
obs--76.04 %

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