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- PDB-6j4d: Crystal structure of MarH, an epimerase for biosynthesis of Marem... -

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Basic information

Entry
Database: PDB / ID: 6j4d
TitleCrystal structure of MarH, an epimerase for biosynthesis of Maremycins in Streptomyces, under pH 4.7, without Zn
ComponentsCupin superfamily protein
KeywordsISOMERASE / epimerase / Maremycins / biosynthesis
Function / homologyRmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / CITRATE ANION / Cupin superfamily protein
Function and homology information
Biological speciesStreptomyces sp. B9173 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHou, Y. / Liu, B. / Hu, K. / Zhang, R.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0505800 China
National Basic Research Program of China (973 Program)2017YFA0504300 China
National Natural Science Foundation of China31570720 China
CitationJournal: To Be Published
Title: Structural Basis for the Isomerization Mechanism of MarH
Authors: Liu, B. / Hou, Y. / Zhang, R. / Hu, K.
History
DepositionJan 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cupin superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6043
Polymers13,3231
Non-polymers2812
Water2,126118
1
A: Cupin superfamily protein
hetero molecules

A: Cupin superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2096
Polymers26,6472
Non-polymers5624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4610 Å2
ΔGint-34 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.425, 43.425, 98.383
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cupin superfamily protein


Mass: 13323.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. B9173 (bacteria) / Gene: marH / Production host: Escherichia coli (E. coli) / References: UniProt: X2D812
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM sodium citrate, pH4.7, 20% PEG3350, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 18801 / % possible obs: 98.5 % / Redundancy: 14 % / Net I/σ(I): 54.3
Reflection shellResolution: 1.4→1.42 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→37.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.757 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.167 965 5.1 %RANDOM
Rwork0.1454 ---
obs0.1465 17789 85.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.6 Å2 / Biso mean: 10.862 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.4→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 19 118 1047
Biso mean--15.92 21.92 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.019951
X-RAY DIFFRACTIONr_bond_other_d0.0020.02914
X-RAY DIFFRACTIONr_angle_refined_deg2.3262.021298
X-RAY DIFFRACTIONr_angle_other_deg0.95932113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92623.61136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47315139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.978155
X-RAY DIFFRACTIONr_chiral_restr0.1420.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02193
LS refinement shellResolution: 1.4→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 11 -
Rwork0.164 348 -
all-359 -
obs--22.94 %

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