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- PDB-3tf0: Crystal structure of an H-NOX protein from T. tengcongensis -

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Basic information

Entry
Database: PDB / ID: 3tf0
TitleCrystal structure of an H-NOX protein from T. tengcongensis
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / Heme-based Methyl-accepting Chemotaxis Protein / Gas Binding
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å
AuthorsWinter, M.B. / Herzik Jr., M.A. / Kuriyan, J. / Marletta, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain.
Authors: Winter, M.B. / Herzik, M.A. / Kuriyan, J. / Marletta, M.A.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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_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: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4517
Polymers44,0952
Non-polymers1,3565
Water2,000111
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7554
Polymers22,0481
Non-polymers7083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6963
Polymers22,0481
Non-polymers6482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.502, 130.766, 42.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHIS PROTEIN EXISTS AS A MONOMER IN SOLUTION AS CONFIRMED BY GEL FILTRATION

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Components

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


Mass: 22047.502 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP Residues 1-186)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-28% PEG 2000, 200-250 mM Sodium Acetate (pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2010
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.743→50 Å / Num. all: 43735 / Num. obs: 43735 / % possible obs: 93.09 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.743→1.8 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U4H

1u4h


Resolution: 1.743→38.47 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 2206 5.04 %
Rwork0.202 --
obs0.2034 43735 93.09 %
all-43735 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.792 Å2 / ksol: 0.412 e/Å3
Refinement stepCycle: LAST / Resolution: 1.743→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 94 111 3277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083278
X-RAY DIFFRACTIONf_angle_d0.9924441
X-RAY DIFFRACTIONf_dihedral_angle_d13.5961254
X-RAY DIFFRACTIONf_chiral_restr0.064457
X-RAY DIFFRACTIONf_plane_restr0.004557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.743-1.78090.31121030.31442203X-RAY DIFFRACTION79
1.7809-1.82240.35011310.26272290X-RAY DIFFRACTION85
1.8224-1.86790.2881080.22852409X-RAY DIFFRACTION86
1.8679-1.91840.24221300.22492431X-RAY DIFFRACTION89
1.9184-1.97490.26761140.22572491X-RAY DIFFRACTION90
1.9749-2.03860.26821400.21672573X-RAY DIFFRACTION93
2.0386-2.11150.28321520.21622576X-RAY DIFFRACTION94
2.1115-2.1960.23791290.20152628X-RAY DIFFRACTION95
2.196-2.2960.24381510.19552649X-RAY DIFFRACTION96
2.296-2.4170.22371500.18712664X-RAY DIFFRACTION97
2.417-2.56840.23771270.19852706X-RAY DIFFRACTION97
2.5684-2.76670.24761580.20182709X-RAY DIFFRACTION97
2.7667-3.0450.24161560.21542745X-RAY DIFFRACTION98
3.045-3.48530.23351620.21172734X-RAY DIFFRACTION98
3.4853-4.39020.19571490.1832815X-RAY DIFFRACTION98
4.3902-38.47910.18981460.18772906X-RAY DIFFRACTION97
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)
10.61650.39460.22631.61620.45720.8492-0.0577-0.06890.1454-0.0541-0.04450.183-0.15590.1323-0.03510.195-0.02050.02780.17970.02190.190868.015321.059923.0598
23.2289-0.2198-0.0571.45990.58590.25040.12630.4288-0.207-0.0378-0.1718-0.0943-0.04120.0791-0.01030.2535-0.01820.02410.2815-0.0130.233877.401418.256815.1961
33.0250.3113-0.05331.04030.1222.07520.05840.16680.48080.0066-0.1023-0.13660.02080.4650.02430.26680.01420.01080.3230.04990.27267.254227.405113.9355
40.9143-0.2959-0.3041.06840.32150.5598-0.14050.3014-0.5264-0.4239-0.0222-0.13170.1478-0.0218-0.07770.2620.01260.06380.237-0.07070.273269.237611.922815.0923
51.74320.0197-0.42690.3563-0.61861.1665-0.1077-0.2279-0.45030.1973-0.0852-0.04670.07580.17860.10440.1713-0.02640.02750.1810.00730.224566.2316.118628.3931
60.1437-0.02940.07940.8653-0.53750.4243-0.1826-0.0970.03920.4158-0.0878-0.0023-0.3173-0.0712-0.13570.31610.03360.05250.2348-0.15090.32658.429327.228337.7828
70.413-0.4442-0.08181.040.59140.76960.043-0.10110.0601-0.1156-0.10760.2978-0.2037-0.1847-0.02170.18910.01560.05360.1791-0.07360.290350.960722.62533.5375
80.49460.33330.58180.35060.49790.9093-0.1791-0.07030.0207-0.0387-0.03360.4431-0.2681-0.0375-0.02560.20320.02180.0080.2012-0.01680.293848.223821.437725.4847
90.4655-0.10880.01560.07450.19771.0227-0.04860.0348-0.1982-0.0353-0.03140.1533-0.021-0.2140.05380.1955-0.03950.05820.2235-0.03970.245350.237211.903628.4109
101.1049-0.1678-0.27761.90040.811.3559-0.1056-0.1541-0.4724-0.1888-0.14630.01220.01020.03010.03550.142-0.02720.0520.16640.03510.195259.912513.612732.767
110.38320.1488-0.33261.1220.22822.0919-0.2682-0.2323-0.3451-0.0356-0.12160.2679-0.00690.1390.10540.2226-0.02110.05290.22830.03090.394754.17586.855534.6234
120.249-0.14940.34810.3672-0.07520.77820.11090.0628-0.0317-0.0491-0.10270.47020.3466-0.12520.00650.2271-0.01720.03330.19620.00580.453348.07838.486329.343
130.10520.0421-0.09020.0157-0.03720.07420.07650.04520.10420.05270.09630.0252-0.2327-0.11460.07540.37780.08620.72180.493-0.05680.220446.206814.521349.3177
141.125-0.1008-0.62210.3553-0.0550.7526-0.054-0.4567-0.10070.12780.0251-0.06110.12580.35540.0160.2058-0.0053-0.0310.31860.03150.199573.926-19.073731.6454
150.85890.90470.26451.30850.931.2756-0.0141-0.1338-0.49090.22540.1643-0.34880.20740.5408-0.07090.29050.0293-0.02120.49390.08030.373469.3772-26.314238.1792
160.87820.19730.81911.87710.71960.928-0.1247-0.42570.28850.57410.277-0.26490.0824-0.0835-0.05160.2647-0.0009-0.04740.4259-0.09690.210671.6892-10.798936.4455
170.3882-0.2523-0.08140.4237-0.02330.1089-0.02840.04480.1547-0.17760.0727-0.2648-0.03920.1336-0.01770.15330.0147-0.01440.211-0.02040.227568.2984-15.774222.8869
180.23080.02210.00660.36330.66931.5563-0.11790.108-0.22640.104-0.09640.07220.41290.0277-0.10130.2201-0.0169-0.06440.1792-0.0850.287459.9766-26.834914.2501
190.5367-0.15570.06890.74530.21530.37750.10750.0036-0.1923-0.1099-0.21210.6193-0.0385-0.24470.01590.18750.0157-0.05530.2159-0.03210.322854.3714-16.336221.647
200.90830.6021-0.07161.5225-0.15440.01830.0869-0.09290.2088-0.3522-0.08440.5820.1480.43620.01340.27610.0852-0.04480.32260.01740.274353.3272-6.505719.2099
210.19010.0279-0.00530.02970.03120.0270.03160.0175-0.0656-0.02940.0626-0.03230.14510.276-0.00060.50870.2798-0.35040.796-0.15660.507144.1461-16.27563.4518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:17)
2X-RAY DIFFRACTION2chain 'A' and (resseq 18:29)
3X-RAY DIFFRACTION3chain 'A' and (resseq 30:44)
4X-RAY DIFFRACTION4chain 'A' and (resseq 45:62)
5X-RAY DIFFRACTION5chain 'A' and (resseq 63:81)
6X-RAY DIFFRACTION6chain 'A' and (resseq 82:90)
7X-RAY DIFFRACTION7chain 'A' and (resseq 91:104)
8X-RAY DIFFRACTION8chain 'A' and (resseq 105:123)
9X-RAY DIFFRACTION9chain 'A' and (resseq 124:137)
10X-RAY DIFFRACTION10chain 'A' and (resseq 138:152)
11X-RAY DIFFRACTION11chain 'A' and (resseq 153:165)
12X-RAY DIFFRACTION12chain 'A' and (resseq 166:178)
13X-RAY DIFFRACTION13chain 'A' and (resseq 179:186)
14X-RAY DIFFRACTION14chain 'B' and (resseq 1:29)
15X-RAY DIFFRACTION15chain 'B' and (resseq 30:44)
16X-RAY DIFFRACTION16chain 'B' and (resseq 45:62)
17X-RAY DIFFRACTION17chain 'B' and (resseq 63:81)
18X-RAY DIFFRACTION18chain 'B' and (resseq 82:90)
19X-RAY DIFFRACTION19chain 'B' and (resseq 91:152)
20X-RAY DIFFRACTION20chain 'B' and (resseq 153:178)
21X-RAY DIFFRACTION21chain 'B' and (resseq 179:188)

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