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- PDB-4qsz: Crystal structure of mouse JMJd7 fused with maltose-binding protein -

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Basic information

Entry
Database: PDB / ID: 4qsz
TitleCrystal structure of mouse JMJd7 fused with maltose-binding protein
ComponentsMaltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera
KeywordsTRANSCRIPTION / Demethylase
Function / homology
Function and homology information


peptidyl-lysine (3S)-dioxygenase / peptidyl-lysine 3-dioxygenase activity / Protein hydroxylation / 2-oxoglutarate-dependent dioxygenase activity / Hydrolases; Acting on peptide bonds (peptidases) / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport ...peptidyl-lysine (3S)-dioxygenase / peptidyl-lysine 3-dioxygenase activity / Protein hydroxylation / 2-oxoglutarate-dependent dioxygenase activity / Hydrolases; Acting on peptide bonds (peptidases) / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / aminopeptidase activity / methylated histone binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / monooxygenase activity / outer membrane-bounded periplasmic space / endopeptidase activity / periplasmic space / DNA damage response / proteolysis / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / RmlC-like jelly roll fold
Similarity search - Domain/homology
CITRATE ANION / alpha-D-glucopyranose / Maltose/maltodextrin-binding periplasmic protein / Bifunctional peptidase and (3S)-lysyl hydroxylase Jmjd7
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsLiu, H. / Wang, C. / Zhang, G.Y.
CitationJournal: To be Published
Title: Crystal structure of mouse JMJd7 fused with maltose-binding protein
Authors: Liu, H. / Zhang, G.
History
DepositionJul 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera
B: Maltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2148
Polymers153,1152
Non-polymers1,0996
Water0
1
A: Maltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1074
Polymers76,5581
Non-polymers5493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1074
Polymers76,5581
Non-polymers5493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-25 kcal/mol
Surface area53450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.090, 158.920, 100.010
Angle α, β, γ (deg.)90.00, 94.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera / MBP / MMBP / Maltodextrin-binding protein / Jumonji domain-containing protein 7 / Jmjd7


Mass: 76557.555 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Mus musculus (house mouse)
Gene: malE, b4034, JW3994, Jmjd7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P0C872
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
Sequence detailsPROTEIN IS A CHIMERA COMPRISING RESIDUES 27-387 OF MBP (UNP P0AEX9) AND RESIDUES 2-312 OF JMJD7 ...PROTEIN IS A CHIMERA COMPRISING RESIDUES 27-387 OF MBP (UNP P0AEX9) AND RESIDUES 2-312 OF JMJD7 (UNP P0C872) CONNECTED BY AN AAAQTNAAAEF LINKER.

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8
Details: Hampton Research PEG/ION HT (89): 20 mM sodium citrate, 80 mM Bis-Tris propane, 16% PEG3350, pH 8.0, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 28, 2014
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→100 Å / Num. all: 46852 / Num. obs: 44978 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.59→2.68 Å / % possible all: 91

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→62.153 Å / SU ML: 0.39 / σ(F): 1.04 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1680 4.98 %RANDOM
Rwork0.1912 ---
obs0.1948 33755 97.67 %-
all-34560 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→62.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 72 0 10832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111135
X-RAY DIFFRACTIONf_angle_d1.38315194
X-RAY DIFFRACTIONf_dihedral_angle_d15.624046
X-RAY DIFFRACTIONf_chiral_restr0.0531652
X-RAY DIFFRACTIONf_plane_restr0.0061971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.94420.33441320.24832588X-RAY DIFFRACTION96
2.9442-3.03930.31631420.25052533X-RAY DIFFRACTION93
3.0393-3.14790.32931270.24662554X-RAY DIFFRACTION93
3.1479-3.27390.33371500.24612638X-RAY DIFFRACTION97
3.2739-3.42290.32271360.22572778X-RAY DIFFRACTION100
3.4229-3.60330.29021400.20962691X-RAY DIFFRACTION100
3.6033-3.82910.26411440.19332727X-RAY DIFFRACTION100
3.8291-4.12470.21711400.17142714X-RAY DIFFRACTION100
4.1247-4.53960.25231410.15292725X-RAY DIFFRACTION99
4.5396-5.19630.2251450.14932699X-RAY DIFFRACTION99
5.1963-6.54560.24541450.17452722X-RAY DIFFRACTION99
6.5456-62.16740.20321380.16472706X-RAY DIFFRACTION97

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