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- PDB-6bdd: Crystal structure of Fe(II) unliganded H-NOX protein from K. algicida -

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Basic information

Entry
Database: PDB / ID: 6bdd
TitleCrystal structure of Fe(II) unliganded H-NOX protein from K. algicida
Components2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
KeywordsSIGNALING PROTEIN / Nitric oxide signaling / heme nitric oxide/oxygen sensing protein
Function / homologyHeme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Function and homology information
Biological speciesKordia algicida OT-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å
AuthorsBruegger, J.J. / Hespen, C.W. / Marletta, M.A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins.
Authors: Hespen, C.W. / Bruegger, J.J. / Guo, Y. / Marletta, M.A.
History
DepositionOct 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9012
Polymers21,2841
Non-polymers6161
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.966, 57.613, 68.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase


Mass: 21284.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kordia algicida OT-1 (bacteria) / Gene: KAOT1_17313 / Production host: Escherichia coli (E. coli) / References: UniProt: A9DSJ8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.28 Å3/Da / Density % sol: 46.04 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.3 M LiCl, 34% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→44.17 Å / Num. obs: 15750 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 34.58 Å2 / CC1/2: 0.616 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.78
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 692 / % possible all: 91.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BOSdata collection
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U99

4u99


Resolution: 1.901→44.17 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2421 807 5.14 %
Rwork0.1927 --
obs0.1951 15708 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.36 Å2 / Biso mean: 42.7677 Å2 / Biso min: 19.91 Å2
Refinement stepCycle: final / Resolution: 1.901→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 43 129 1668
Biso mean--31.9 47.61 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021576
X-RAY DIFFRACTIONf_angle_d0.6482141
X-RAY DIFFRACTIONf_chiral_restr0.039236
X-RAY DIFFRACTIONf_plane_restr0.001267
X-RAY DIFFRACTIONf_dihedral_angle_d5.021925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9012-2.02040.34531080.25652342245095
2.0204-2.17640.24471460.221324382584100
2.1764-2.39540.2941620.213624482610100
2.3954-2.74190.24671220.203925022624100
2.7419-3.45430.26561440.212325142658100
3.4543-44.18190.20211250.166926572782100
Refinement TLS params.Method: refined / Origin x: 2.795 Å / Origin y: -6.862 Å / Origin z: -2.044 Å
111213212223313233
T0.2298 Å2-0.0221 Å2-0.0192 Å2-0.2257 Å20.0143 Å2--0.2141 Å2
L2.7195 °2-0.0179 °2-0.1416 °2-0.7643 °20.0621 °2--1.3116 °2
S0.0343 Å °0.2602 Å °0.1845 Å °-0.0083 Å °-0.1278 Å °0.0142 Å °-0.0455 Å °0.0369 Å °-0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:185 OR RESID 201:201 OR RESID 301:429 ) )A1 - 185
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:185 OR RESID 201:201 OR RESID 301:429 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:185 OR RESID 201:201 OR RESID 301:429 ) )A301 - 429

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