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- PDB-4mhu: Crystal structure of EctD from S. alaskensis with bound Fe -

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Basic information

Entry
Database: PDB / ID: 4mhu
TitleCrystal structure of EctD from S. alaskensis with bound Fe
ComponentsEctoine hydroxylase
KeywordsOXIDOREDUCTASE / jelly-roll or cupin fold / ectoine hydroxylase / ectoine
Function / homology
Function and homology information


ectoine hydroxylase / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Ectoine dioxygenase / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-DODECYL-N,N-DIMETHYLGLYCINATE / : / Ectoine dioxygenase
Similarity search - Component
Biological speciesSphingopyxis alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWidderich, N. / Hoeppner, A. / Pittelkow, M. / Heider, J. / Smits, S.H. / Bremer, E.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of the ectoine hydroxylase, a snapshot of the active site.
Authors: Hoppner, A. / Widderich, N. / Lenders, M. / Bremer, E. / Smits, S.H.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ectoine hydroxylase
B: Ectoine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8365
Polymers70,4532
Non-polymers3833
Water00
1
A: Ectoine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2822
Polymers35,2271
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ectoine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5543
Polymers35,2271
Non-polymers3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ectoine hydroxylase
hetero molecules

B: Ectoine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8365
Polymers70,4532
Non-polymers3833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_464-x-1/2,-y+1,z-1/21
Buried area2490 Å2
ΔGint-40 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.165, 87.519, 96.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.852941, -0.521755, -0.016217), (-0.521633, -0.853094, 0.011388), (-0.019776, -0.001254, -0.999804)19.98173, 70.67481, -0.96353

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Components

#1: Protein Ectoine hydroxylase


Mass: 35226.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis alaskensis (bacteria) / Strain: DSM 13593 / LMG 18877 / RB2256 / Gene: Sala_2952 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GNW5
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-D9G / N-DODECYL-N,N-DIMETHYLGLYCINATE


Mass: 271.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H33NO2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES (pH 6.0), 200 mM Ca-acetate, 15-30 % (w/v) PEG 400 and 1.5-3.5 mM n-dodecyl-N N-dimethylglycine, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.56→46 Å / Num. all: 21776 / Num. obs: 20668 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.56→2.63 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.024 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26624 1112 5.1 %RANDOM
Rwork0.20206 ---
obs0.20529 20668 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0 Å2
2--3.54 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.56→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 21 0 4398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194507
X-RAY DIFFRACTIONr_bond_other_d0.0010.024246
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9566129
X-RAY DIFFRACTIONr_angle_other_deg0.79639724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61522.785219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90615682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4181545
X-RAY DIFFRACTIONr_chiral_restr0.0790.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021076
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.56→2.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 86 -
Rwork0.305 1487 -
obs--99.87 %

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