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- PDB-6bde: Crystal structure of Fe(II) unliganded H-NOX protein mutant A71G ... -

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Basic information

Entry
Database: PDB / ID: 6bde
TitleCrystal structure of Fe(II) unliganded H-NOX protein mutant A71G 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 / 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 / Resolution: 1.641 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)21,8872
Polymers21,2701
Non-polymers6161
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.794, 56.730, 68.753
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: 21270.156 Da / Num. of mol.: 1 / Mutation: A71G
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 / Heme B


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


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.24 Å3/Da / Density % sol: 45.01 % / Description: Rod
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% 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 PILATUS 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: 1.64→50 Å / Num. obs: 23704 / % possible obs: 99.5 % / Redundancy: 12.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Χ2: 1.009 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.64-1.688.30.5311330.950.1860.5640.94896.3
1.68-1.719.80.50111580.9550.1670.531.0199.8
1.71-1.7411.30.47911780.9690.1480.5021.005100
1.74-1.78120.4111490.9740.1240.4281.051100
1.78-1.8212.10.3411930.9830.1030.3561.01599.9
1.82-1.8612.20.2911470.9880.0870.3031.011100
1.86-1.912.30.23411800.9920.0690.2441.01399.9
1.9-1.9612.70.20311900.9910.0590.2121.014100
1.96-2.0112.90.17511630.9930.050.1821.008100
2.01-2.0813.20.15611780.9930.0440.1621.04299.8
2.08-2.1512.90.14111740.9950.0410.1471.007100
2.15-2.2412.50.12911830.9950.0380.1340.955100
2.24-2.3412.90.11811920.9930.0340.1231.00599.9
2.34-2.4612.80.11111750.9960.0320.1160.96100
2.46-2.6213.30.10112060.9950.0290.1051.052100
2.62-2.8212.90.09411940.9970.0270.0981.038100
2.82-3.1112.40.08911960.9960.0260.0931.01199.7
3.11-3.5512.90.0812130.9960.0230.0831.03199.4
3.55-4.48120.07411980.9960.0220.0771.04296.9
4.48-5011.70.06713040.9970.0210.070.94298.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BDD

6bdd


Resolution: 1.641→39.791 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.54
RfactorNum. reflection% reflection
Rfree0.2362 1183 5.01 %
Rwork0.2103 --
obs0.2117 23631 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.22 Å2 / Biso mean: 47.4573 Å2 / Biso min: 24.72 Å2
Refinement stepCycle: final / Resolution: 1.641→39.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 43 126 1664
Biso mean--35.95 52.05 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051575
X-RAY DIFFRACTIONf_angle_d2.8162139
X-RAY DIFFRACTIONf_chiral_restr0.04235
X-RAY DIFFRACTIONf_plane_restr0.003267
X-RAY DIFFRACTIONf_dihedral_angle_d6.256933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6412-1.71590.35731460.28642539268591
1.7159-1.80640.28611350.264927892924100
1.8064-1.91960.31011420.253428212963100
1.9196-2.06780.27461510.233327972948100
2.0678-2.27580.23191540.227628322986100
2.2758-2.60510.24631270.225728652992100
2.6051-3.28190.27931630.230428613024100
3.2819-39.80310.21650.18212944310998
Refinement TLS params.Method: refined / Origin x: 2.6513 Å / Origin y: -6.7623 Å / Origin z: -1.8656 Å
111213212223313233
T0.2267 Å2-0.0257 Å2-0.048 Å2-0.2843 Å20.0248 Å2--0.2305 Å2
L4.3661 °2-0.0623 °20.1251 °2-1.7139 °20.2128 °2--2.4037 °2
S-0.1545 Å °0.3779 Å °0.2852 Å °-0.0619 Å °-0.074 Å °0.1034 Å °-0.1507 Å °0.016 Å °0.1907 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 185
2X-RAY DIFFRACTION1allA186
3X-RAY DIFFRACTION1allS1 - 139

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