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- PDB-7x98: 5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris -

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Basic information

Entry
Database: PDB / ID: 7x98
Title5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris
Components5-aminolevulinate synthase
KeywordsTRANSFERASE / PLP dependent enzyme
Function / homology
Function and homology information


5-aminolevulinate synthase / 5-aminolevulinate synthase activity / protoporphyrinogen IX biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
5-aminolevulinate synthase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhang, T.T. / Liu, H.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of 5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris presents multiple conformations.
Authors: Zhang, T. / Chen, J. / Zheng, P. / Gong, W. / Sun, J. / Liu, H.
History
DepositionMar 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-aminolevulinate synthase
B: 5-aminolevulinate synthase
C: 5-aminolevulinate synthase
D: 5-aminolevulinate synthase


Theoretical massNumber of molelcules
Total (without water)175,8614
Polymers175,8614
Non-polymers00
Water16,051891
1
A: 5-aminolevulinate synthase
B: 5-aminolevulinate synthase


Theoretical massNumber of molelcules
Total (without water)87,9312
Polymers87,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-45 kcal/mol
Surface area26040 Å2
MethodPISA
2
C: 5-aminolevulinate synthase
D: 5-aminolevulinate synthase


Theoretical massNumber of molelcules
Total (without water)87,9312
Polymers87,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-44 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.157, 68.896, 85.639
Angle α, β, γ (deg.)82.020, 85.260, 66.060
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
5-aminolevulinate synthase / 5-aminolevulinic acid synthase / Delta-ALA synthase / Delta-aminolevulinate synthase


Mass: 43965.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: hemA, HUU61_06935 / Production host: Escherichia coli (E. coli) / References: UniProt: M1FRN3, 5-aminolevulinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Bis-Tris pH 6.5, Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 82589 / % possible obs: 94.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.614 / Net I/σ(I): 14.2 / Num. measured all: 303616
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.05-2.123.70.17880840.667192.6
2.12-2.213.70.14981450.779193
2.21-2.313.70.12882170.875193.5
2.31-2.433.70.1181971.049193.9
2.43-2.583.70.09583051.206194.6
2.58-2.783.70.08483001.464195.2
2.78-3.063.70.07184051.833195.7
3.06-3.513.60.05983702.397195.8
3.51-4.423.50.05182412.889194.1
4.42-503.50.04883253.162195

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BWN

2bwn


Resolution: 2.05→34.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.978 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 4148 5 %RANDOM
Rwork0.1518 ---
obs0.1544 78440 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.74 Å2 / Biso mean: 25.655 Å2 / Biso min: 10.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.42 Å20.69 Å2
2---0.84 Å2-0.23 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.05→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12226 0 0 891 13117
Biso mean---30.63 -
Num. residues----1598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312549
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711538
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.63517066
X-RAY DIFFRACTIONr_angle_other_deg1.3951.57226485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62251610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09720.157701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.925151898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.70315124
X-RAY DIFFRACTIONr_chiral_restr0.0730.21623
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022978
LS refinement shellResolution: 2.05→2.098 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.231 273 -
Rwork0.165 5523 -
obs--89.35 %

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