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- PDB-3eee: Probing the function of heme distortion in the H-NOX family -

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Basic information

Entry
Database: PDB / ID: 3eee
TitleProbing the function of heme distortion in the H-NOX family
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / Hemoprotein
Function / homology
Function and homology information


heme binding / signal transduction / metal ion binding / membrane
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 / OXYGEN MOLECULE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.12 Å
AuthorsOlea Jr, C. / Boon, E.M. / Pellicena, P. / Kuriyan, J. / Marletta, M.A.
CitationJournal: Acs Chem.Biol. / Year: 2008
Title: Probing the function of heme distortion in the H-NOX family.
Authors: Olea, C. / Boon, E.M. / Pellicena, P. / Kuriyan, J. / Marletta, M.A.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Methyl-accepting chemotaxis protein
D: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,03917
Polymers88,0864
Non-polymers2,95313
Water3,171176
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7664
Polymers22,0211
Non-polymers7453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8015
Polymers22,0211
Non-polymers7804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7054
Polymers22,0211
Non-polymers6843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7664
Polymers22,0211
Non-polymers7453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.253, 124.686, 83.555
Angle α, β, γ (deg.)90.00, 126.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Methyl-accepting chemotaxis protein


Mass: 22021.465 Da / Num. of mol.: 4 / Fragment: H-NOX Domain, residues 1-188 / Mutation: P115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Gene: Tar4 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBX6

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Non-polymers , 5 types, 189 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 289 K / pH: 9.1
Details: 0.1 M NaSCN, 0.1 M Tris pH 9.1, 0.2 M (NH4)2(SO4), and 18% (w/v) PEG 8000 at 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 53717 / Num. obs: 53717 / Redundancy: 4.3 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementStarting model: PDB entry 1U55

1u55


Resolution: 2.12→45.672 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 2704 5.09 %
Rwork0.2048 --
obs0.2071 53135 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.515 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 67.643 Å2
Baniso -1Baniso -2Baniso -3
1-10.734 Å2-0 Å2-3.094 Å2
2---2.968 Å2-0 Å2
3----7.766 Å2
Refinement stepCycle: LAST / Resolution: 2.12→45.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6184 0 197 176 6557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086522
X-RAY DIFFRACTIONf_angle_d0.8988804
X-RAY DIFFRACTIONf_dihedral_angle_d17.2362444
X-RAY DIFFRACTIONf_chiral_restr0.053904
X-RAY DIFFRACTIONf_plane_restr0.0031094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.15830.35041250.30292211X-RAY DIFFRACTION83
2.1583-2.19980.3181310.28232710X-RAY DIFFRACTION99
2.1998-2.24470.33991510.26722673X-RAY DIFFRACTION99
2.2447-2.29350.34541390.27222655X-RAY DIFFRACTION99
2.2935-2.34690.28141550.25822667X-RAY DIFFRACTION100
2.3469-2.40550.32991500.25192687X-RAY DIFFRACTION100
2.4055-2.47060.28971760.24922635X-RAY DIFFRACTION100
2.4706-2.54330.33171270.24852740X-RAY DIFFRACTION100
2.5433-2.62540.28031430.23562688X-RAY DIFFRACTION100
2.6254-2.71920.30841430.2422688X-RAY DIFFRACTION100
2.7192-2.8280.27931510.2342682X-RAY DIFFRACTION100
2.828-2.95670.27311360.22582706X-RAY DIFFRACTION99
2.9567-3.11260.27171290.2242671X-RAY DIFFRACTION100
3.1126-3.30750.26241500.21862696X-RAY DIFFRACTION100
3.3075-3.56280.26231470.20162705X-RAY DIFFRACTION99
3.5628-3.92120.22081340.17872681X-RAY DIFFRACTION99
3.9212-4.48820.20361610.16762642X-RAY DIFFRACTION98
4.4882-5.65290.20771260.15942687X-RAY DIFFRACTION98
5.6529-45.68280.21361300.18022607X-RAY DIFFRACTION94
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)
12.84820.8366-0.3563.3577-1.7203-0.0551-0.3129-1.0649-0.00590.48930.07960.04430.18020.29010.24040.65730.0248-0.00140.5510.00770.3330.9378-19.61220.4187
23.7224-0.56821.7299-1.504-1.31255.4837-0.19830.0184-0.20630.23470.0786-0.05580.59750.80810.24830.50090.0422-0.0250.40460.08740.432429.9555-19.95515.1598
32.63320.6073-0.55763.4979-0.27549.1236-0.0939-0.2328-0.3588-0.2674-0.36980.20630.83280.43120.40880.4594-0.00220.02170.3112-0.02280.350317.4134-25.92162.2653
44.7994-0.1209-2.04972.3639-2.61228.9183-0.52490.00650.3412.0671-0.15970.8608-0.5282-0.54940.49710.8560.07290.27680.5117-0.11610.400911.7462-20.8748.2734
52.11531.8113-0.01692.8639-1.88191.0357-0.07530.07670.124-0.22820.0531-0.0134-0.1801-0.09020.01780.47570.049-0.04740.3514-0.00690.300817.9441-13.3624-2.9589
62.05381.1260.781.0992-1.33881.6844-0.3362-0.6245-0.09170.42920.16420.0173-0.16850.16050.18410.64910.07810.00690.43260.0170.335711.5263-19.260356.1188
71.77520.44492.03572.6831-0.61424.77750.04830.1112-0.02240.0284-0.38940.02440.030.61480.4390.4440.0688-0.03060.41250.06020.386110.0933-20.409140.6038
81.5780.21592.13663.761-2.41310.6804-0.1343-0.1492-0.3388-0.021-0.25470.48820.4178-0.15010.37110.5105-0.02010.08060.3657-0.05350.4365-3.0061-25.22839.202
92.6732-2.04190.05574.3791-0.6993-1.06720.11890.19620.08750.071-0.26960.1235-0.3402-0.00440.1410.4990.0402-0.00770.4315-0.0150.2748-1.0031-12.81636.4643
102.8512.31690.61860.72390.84778.4196-0.17350.51080.1114-0.36590.3713-0.03650.03960.3674-0.24150.69710.2072-0.07620.471-0.01160.3677-4.3863-14.679323.7612
11-0.31332.9185-2.08125.00481.6762.167-0.29430.56230.6229-1.17630.6947-0.4154-0.42590.6151-0.44260.7481-0.0861-0.01570.80130.03091.109227.635919.302520.0719
121.31351.9365-0.82072.63142.48541.3949-0.0457-0.17390.16830.0186-0.02610.2288-0.4887-0.08570.0730.6839-0.03730.00420.32540.00190.4568.675917.842220.6794
138.97864.7757-3.3438-3.33840.3538-0.646-0.8801-0.66850.5804-0.71162.15970.05560.11180.1909-1.19670.8467-0.26660.05742.03240.03871.768114.067822.12812.4346
140.6768-0.2731.13272.87230.07491.17410.0287-0.0891-0.22270.1579-0.0907-0.30210.1350.07020.07940.6152-0.03610.10740.3647-0.01690.52534.89137.157217.059
15-1.4673-0.4269-1.97312.0165-3.3491-4.2745-0.01151.04890.3187-0.58041.2554-0.99720.0381-0.11-0.38040.71150.16330.01371.0837-0.13371.2165-16.767212.189714.3038
164.5131-0.02060.43753.6252-0.53343.16450.2880.40110.08450.1366-0.15930.2263-0.05-0.5936-0.13540.43030.00550.02580.45320.00350.39216.1063-44.875511.433
17-0.18163.14120.89982.753-0.81636.22970.6579-0.27890.65960.6102-0.1052-1.1213-1.02320.7833-0.44250.6533-0.05330.01030.45820.04570.610926.4847-43.621817.0488
180.7012-5.234-0.3448-0.12134.95842.0657-0.2469-0.2627-3.4233-0.72960.1323-0.666-0.4010.0150.16941.9107-0.06730.0981.01950.45731.717315.6988-40.253829.7751
192.9895-1.0517-0.48844.1646-0.4853.8625-0.02130.0578-0.40010.1552-0.1865-0.14710.33740.06470.190.40930.01060.03980.29330.02190.413123.3341-55.219515.6011
20-3.3315-3.4842-2.7137.5696-1.64793.9758-0.29990.14621.13730.2661-0.1678-0.804-0.50650.2238-0.06980.4235-00.07720.83810.04050.79341.605-52.511610.5862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:60)
2X-RAY DIFFRACTION2chain A and resid 61:89)
3X-RAY DIFFRACTION3chain A and resid 90:111)
4X-RAY DIFFRACTION4chain A and resid 112:117)
5X-RAY DIFFRACTION5chain A and resid 118:188)
6X-RAY DIFFRACTION6chain B and resid 1:61)
7X-RAY DIFFRACTION7chain B and resid 62:89)
8X-RAY DIFFRACTION8chain B and resid 90:114)
9X-RAY DIFFRACTION9chain B and resid 115:170)
10X-RAY DIFFRACTION10chain B and resid 171:188)
11X-RAY DIFFRACTION11chain C and resid 1:60)
12X-RAY DIFFRACTION12chain C and resid 61:106)
13X-RAY DIFFRACTION13chain C and resid 107:113)
14X-RAY DIFFRACTION14chain C and resid 114:183)
15X-RAY DIFFRACTION15chain C and resid 184:188)
16X-RAY DIFFRACTION16chain D and resid 1:89)
17X-RAY DIFFRACTION17chain D and resid 90:107)
18X-RAY DIFFRACTION18chain D and resid 108:113)
19X-RAY DIFFRACTION19chain D and resid 114:178)
20X-RAY DIFFRACTION20chain D and resid 179:188)

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