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- PDB-3nvr: Modulating Heme Redox Potential Through Protein-Induced Porphyrin... -

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Basic information

Entry
Database: PDB / ID: 3nvr
TitleModulating Heme Redox Potential Through Protein-Induced Porphyrin Distortion
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / H-NOX / Hemoprotein / Heme cofactor
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 / OXYGEN MOLECULE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsOlea Jr., C. / Kuriyan, J. / Marletta, M.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Modulating heme redox potential through protein-induced porphyrin distortion
Authors: Olea, C. / Kuriyan, J. / Marletta, M.A.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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)45,4638
Polymers44,0952
Non-polymers1,3686
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-79 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.825, 126.095, 42.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 Donaim / Mutation: I5L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter 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-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 26% PEG 4000, 0.05 M MES pH 6, 0.1 M LiCl, VAPOR DIFFUSION, SITTING DROP, temperature 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 315r / Detector: CCD / Date: Nov 8, 2007
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 24174 / Num. obs: 24124 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rsym value: 0.06 / Net I/σ(I): 24.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 4.75 / Num. unique all: 2359 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.148→49.477 Å / SU ML: 0.34 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1229 5.09 %Random
Rwork0.2172 ---
obs0.2194 23163 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.026 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1596 Å20 Å20 Å2
2--5.7081 Å2-0 Å2
3---2.4516 Å2
Refinement stepCycle: LAST / Resolution: 2.148→49.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 92 55 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013095
X-RAY DIFFRACTIONf_angle_d1.0354182
X-RAY DIFFRACTIONf_dihedral_angle_d18.3491162
X-RAY DIFFRACTIONf_chiral_restr0.074432
X-RAY DIFFRACTIONf_plane_restr0.008521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1478-2.23380.32711180.2692447X-RAY DIFFRACTION97
2.2338-2.33550.31251480.24472510X-RAY DIFFRACTION100
2.3355-2.45860.2881310.23362517X-RAY DIFFRACTION100
2.4586-2.61260.2811430.23322500X-RAY DIFFRACTION100
2.6126-2.81430.28261370.23282549X-RAY DIFFRACTION100
2.8143-3.09750.26381340.23152554X-RAY DIFFRACTION100
3.0975-3.54560.29951470.22712556X-RAY DIFFRACTION100
3.5456-4.46670.23621430.19352564X-RAY DIFFRACTION99
4.4667-49.48960.21611280.20112698X-RAY DIFFRACTION98
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)
12.0675-0.7866-2.00425.28270.07640.48120.21260.90280.1123-0.8525-0.3217-0.5326-0.18520.20310.13910.42170.0180.07450.62870.0320.3222-10.468519.9952-14.5289
22.5091-0.8017-1.34825.6586-0.27362.7661-0.3111-0.1604-0.32240.59420.19410.7161-0.1402-0.00650.10080.33750.03460.08550.2832-0.01860.3486-24.64616.9555-0.8644
30.8902-3.24490.23937.9726-2.91583.29110.43720.0108-0.8136-0.23770.07872.35020.5531-0.0037-0.14080.3089-0.01030.25120.2790.00290.8409-31.87076.8448-3.2179
41.999622.00012.000422.13660.7211-0.24742.66630.6157-0.7134-2.1801-1.4299-3.00630.02894.8501-1.65361.70910.9132-0.82551.1757-28.396310.742818.3199
52.0919-0.8642-0.6273.57880.33323.59910.0106-0.0786-0.26360.3572-0.0027-0.02020.108-0.1803-0.00650.3181-0.02050.01460.32580.02680.45078.960816.68440.6712
61.25270.5775-0.1481.7492-1.32280.44010.4125-0.0041.2692-0.1059-0.2991-0.8023-0.7462-0.0046-0.07890.48520.12490.17210.31790.15060.613723.544124.8219-12.3123
73.1302-3.2116-0.19177.9708-0.2237-0.64180.28990.0011-0.2137-0.5432-0.5175-0.28820.20740.01240.27320.3430.06530.05310.3610.02760.408125.755110.8869-10.6869
8-1.18846.4533-2.26971.99995.62480.1273-0.30891.2466-0.1875-2.6166-0.375-0.22530.80070.41720.53461.50240.51070.11871.2264-0.17240.997324.38610.6837-24.5777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:61)
2X-RAY DIFFRACTION2(chain A and resid 62:160)
3X-RAY DIFFRACTION3(chain A and resid 161:179)
4X-RAY DIFFRACTION4(chain A and resid 180)
5X-RAY DIFFRACTION5(chain B and resid 1:79)
6X-RAY DIFFRACTION6(chain B and resid 80:108)
7X-RAY DIFFRACTION7(chain B and resid 109:176)
8X-RAY DIFFRACTION8(chain B and resid 177:178)

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