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- PDB-3sj5: I5F Mutant Structure of T. Tengcongensis H-NOX -

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Basic information

Entry
Database: PDB / ID: 3sj5
TitleI5F Mutant Structure of T. Tengcongensis H-NOX
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / NO or O2-sensing protein
Function / homology
Function and homology information


heme binding / signal transduction / membrane / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). ...H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 Å
AuthorsWeinert, E.E. / Phillips-Piro, C.M. / Tran, R. / Mathies, R.A. / Marletta, M.A.
CitationJournal: Biochemistry / Year: 2011
Title: Controlling Conformational Flexibility of an O2-Binding H-NOX Domain.
Authors: Weinert, E.E. / Phillips-Piro, C.M. / Tran, R. / Mathies, R.A. / Marletta, M.A.
History
DepositionJun 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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 / 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 / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3964
Polymers44,1632
Non-polymers1,2332
Water4,756264
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A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6982
Polymers22,0821
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6982
Polymers22,0821
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.585, 67.116, 66.428
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the quaternary structure for the H-NOX domain is monomeric in solution as tested through gel filtration.

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Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 22081.520 Da / Num. of mol.: 2 / Mutation: I5F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus (bacteria)
Strain: subsp. tengcongensis / Gene: Tar4, TTE0680 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): RP523 / References: UniProt: Q8RBX6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 20 % PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 45085 / Num. obs: 45085 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.042 / Net I/σ(I): 31.1
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.355 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.673→47.198 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 2202 5.06 %
Rwork0.1974 --
obs0.1999 43519 96.1 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.208 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4742 Å20 Å20.2541 Å2
2--5.6616 Å20 Å2
3----3.1874 Å2
Refinement stepCycle: LAST / Resolution: 1.673→47.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 86 264 3383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073308
X-RAY DIFFRACTIONf_angle_d0.9924480
X-RAY DIFFRACTIONf_dihedral_angle_d14.8831254
X-RAY DIFFRACTIONf_chiral_restr0.07455
X-RAY DIFFRACTIONf_plane_restr0.005564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.673-1.7090.33471350.26692175X-RAY DIFFRACTION81
1.709-1.74880.30991320.26712378X-RAY DIFFRACTION90
1.7488-1.79250.29721230.24212444X-RAY DIFFRACTION91
1.7925-1.8410.24431310.22512478X-RAY DIFFRACTION93
1.841-1.89520.28921310.20812505X-RAY DIFFRACTION94
1.8952-1.95630.24041580.20142577X-RAY DIFFRACTION96
1.9563-2.02630.2331540.19472612X-RAY DIFFRACTION97
2.0263-2.10740.27661400.18972624X-RAY DIFFRACTION99
2.1074-2.20330.23381300.19472655X-RAY DIFFRACTION99
2.2033-2.31950.26181300.19932680X-RAY DIFFRACTION99
2.3195-2.46480.24721330.20172679X-RAY DIFFRACTION99
2.4648-2.65510.23871550.22648X-RAY DIFFRACTION100
2.6551-2.92220.26721270.2072696X-RAY DIFFRACTION100
2.9222-3.3450.23531430.2042692X-RAY DIFFRACTION100
3.345-4.21390.24721230.18272732X-RAY DIFFRACTION100
4.2139-47.21710.22431570.18132742X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5789-0.2870.04490.61770.00931.32220.1735-0.53860.16280.1109-0.1819-0.2048-0.29130.10130.06430.1133-0.0219-0.03250.33510.01570.209128.459813.408713.5072
20.1911-0.00780.14830.6378-0.13151.1065-0.0024-0.0466-0.02890.01880.0063-0.0012-0.0004-0.27940.01430.09570.01810.00150.1585-0.00880.11818.326110.44744.5469
30.22760.05350.05680.33760.40010.4685-0.00290.3136-0.0037-0.35020.1906-0.0451-0.19360.04840.4870.6351-0.3380.00790.2877-0.23040.180611.59381.2204-32.4435
40.885-0.22970.45310.0993-0.08430.27580.15380.3006-0.20430.0627-0.0389-0.11820.32210.07990.0390.3412-0.03750.02190.1512-0.09130.199118.24397.0886-24.6698
50.1924-0.1168-0.16810.2620.12530.1988-0.01040.21350.0536-0.0547-0.0349-0.0642-0.1482-0.02520.00080.1667-0.00370.00730.1652-0.00160.135421.110823.0471-24.1684
60.14140.0358-0.08290.1122-0.00360.48990.12440.09740.0740.058-0.0532-0.05050.0845-0.02580.00670.17260.0153-0.00240.1153-0.01910.151623.297217.8675-14.9986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:62)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 63:185)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 1:44)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 45:90)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 91:137)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 138:183)

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