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

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Basic information

Entry
Database: PDB / ID: 5dds
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with PLP
ComponentsCrmG
KeywordsTRANSFERASE / Aminotransferase / PLP / Caerulomycin A
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
ACETIC ACID / PYRIDOXAL-5'-PHOSPHATE / CrmG
Similarity search - Component
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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)230,11111
Polymers228,8784
Non-polymers1,2337
Water2,018112
1
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1186
Polymers114,4392
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-47 kcal/mol
Surface area37170 Å2
MethodPISA
2
C: CrmG
D: 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 area10420 Å2
ΔGint-46 kcal/mol
Surface area37030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.078, 84.210, 88.949
Angle α, β, γ (deg.)106.710, 109.160, 95.030
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA7 - 5227 - 522
21GLUGLULEULEUBB7 - 5227 - 522
12GLUGLULEULEUAA7 - 5227 - 522
22GLUGLULEULEUCC7 - 5227 - 522
13GLYGLYLEULEUAA6 - 5226 - 522
23GLYGLYLEULEUDD6 - 5226 - 522
14GLUGLULEULEUBB7 - 5227 - 522
24GLUGLULEULEUCC7 - 5227 - 522
15GLUGLUVALVALBB7 - 5217 - 521
25GLUGLUVALVALDD7 - 5217 - 521
16GLUGLULEULEUCC7 - 5227 - 522
26GLUGLULEULEUDD7 - 5227 - 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.56 %
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: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.925
11-K, -H, -L20.075
ReflectionResolution: 2.6→69.92 Å / Num. obs: 61697 / % possible obs: 92.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.3 / % possible all: 89.5

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimlessdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
Aimlessdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→62.02 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.2495 / WRfactor Rwork: 0.2073 / FOM work R set: 0.8063 / SU B: 10.14 / SU ML: 0.227 / SU Rfree: 0.0785 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.079 / 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
Rfree0.2615 3146 5.1 %RANDOM
Rwork0.2146 ---
obs0.217 58537 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.36 Å2 / Biso mean: 33.739 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--13.64 Å25.55 Å2-0.54 Å2
2--2.63 Å2-6.08 Å2
3---11.01 Å2
Refinement stepCycle: final / Resolution: 2.6→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 0 76 112 16012
Biso mean--33.26 20.03 -
Num. residues----2047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01916169
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215567
X-RAY DIFFRACTIONr_angle_refined_deg0.5781.9721902
X-RAY DIFFRACTIONr_angle_other_deg0.572335612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98452039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02222.855767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.549152695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.62215180
X-RAY DIFFRACTIONr_chiral_restr0.0610.22497
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0218421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023743
X-RAY DIFFRACTIONr_mcbond_it3.4013.2198181
X-RAY DIFFRACTIONr_mcbond_other3.3993.2198179
X-RAY DIFFRACTIONr_mcangle_it5.0214.82710211
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A618520.09
12B618520.09
21A617340.08
22C617340.08
31A621720.08
32D621720.08
41B622440.08
42C622440.08
51B621860.08
52D621860.08
61C617460.09
62D617460.09
LS refinement shellResolution: 2.6→2.6 Å / Total num. of bins used: 20

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