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- PDB-5ddu: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

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Basic information

Entry
Database: PDB / ID: 5ddu
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with PMP
ComponentsCrmG
KeywordsTRANSFERASE / Aminotransferase / PLP / Caerulomycin Biosynthesis
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
TRIETHYLENE GLYCOL / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / CrmG
Similarity search - Component
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsXu, J. / Feng, Z. / Liu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation of China31500638 China
Natural Science Foundation of Guangdong Province2014A030310356 China
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis
Authors: Zhu, Y. / Xu, J. / Mei, X. / Feng, Z. / Zhang, L. / Zhang, Q. / Zhang, G. / Zhu, W. / Liu, J. / Zhang, C.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)230,85018
Polymers228,8784
Non-polymers1,97214
Water5,008278
1
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,54610
Polymers114,4392
Non-polymers1,1078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-50 kcal/mol
Surface area36700 Å2
MethodPISA
2
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3048
Polymers114,4392
Non-polymers8656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-52 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.874, 83.858, 88.438
Angle α, β, γ (deg.)106.660, 109.250, 94.840
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 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVALAA6 - 5216 - 521
21GLYGLYVALVALBB6 - 5216 - 521
12GLYGLYLEULEUAA6 - 5226 - 522
22GLYGLYLEULEUCC6 - 5226 - 522
13SERSERLEULEUAA5 - 5225 - 522
23SERSERLEULEUDD5 - 5225 - 522
14GLYGLYLEULEUBB6 - 5226 - 522
24GLYGLYLEULEUCC6 - 5226 - 522
15GLYGLYVALVALBB6 - 5216 - 521
25GLYGLYVALVALDD6 - 5216 - 521
16GLYGLYLEULEUCC6 - 5226 - 522
26GLYGLYLEULEUDD6 - 5226 - 522

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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG3350, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.928
11-K, -H, -L20.072
ReflectionResolution: 2.46→50.51 Å / Num. obs: 75400 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.947 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.098 / Net I/σ(I): 6.8 / Num. measured all: 262030 / Scaling rejects: 650
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.46-2.513.40.6272.31494343960.590.38196.3
12.3-50.513.80.1213.322785930.9750.06995.2

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.3.11data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
Aimlessdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→50.51 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2325 / WRfactor Rwork: 0.2019 / FOM work R set: 0.8235 / SU B: 16.99 / SU ML: 0.192 / SU R Cruickshank DPI: 0.1731 / SU Rfree: 0.0607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 3750 5 %RANDOM
Rwork0.2065 ---
obs0.2081 71589 88.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.44 Å2 / Biso mean: 19.832 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20.02 Å2-6.18 Å2
2---2.96 Å2-4.37 Å2
3---4.16 Å2
Refinement stepCycle: final / Resolution: 2.46→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15836 0 128 278 16242
Biso mean--35.53 24.62 -
Num. residues----2049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916222
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215651
X-RAY DIFFRACTIONr_angle_refined_deg0.8191.97221962
X-RAY DIFFRACTIONr_angle_other_deg0.68335807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50852041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35922.855767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.939152697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.18915180
X-RAY DIFFRACTIONr_chiral_restr0.0610.22506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218431
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023741
X-RAY DIFFRACTIONr_mcbond_it1.2521.8878188
X-RAY DIFFRACTIONr_mcbond_other1.2521.8878187
X-RAY DIFFRACTIONr_mcangle_it2.0542.82910221
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
11A62648
12B62648
21A62586
22C62586
31A62544
32D62544
41B62434
42C62434
51B62566
52D62566
61C62214
62D62214
LS refinement shellResolution: 2.46→2.46 Å / Total num. of bins used: 20

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