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- PDB-7tt9: Crystal structure of Shewanella benthica Group 1 truncated hemogl... -

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Basic information

Entry
Database: PDB / ID: 7tt9
TitleCrystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y34F variant
ComponentsGroup 1 truncated hemoglobin
KeywordsHEME BINDING PROTEIN / globin / 2/2 hemoglobin / tetramer / piezophilic
Function / homology
Function and homology information


oxygen transport / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesShewanella benthica KT99 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsMartinez, J.E. / Liu, K. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2003950 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N.
Authors: Martinez Grundman, J.E. / Schultz, T.D. / Schlessman, J.L. / Johnson, E.A. / Gillilan, R.E. / Lecomte, J.T.J.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group 1 truncated hemoglobin
B: Group 1 truncated hemoglobin
C: Group 1 truncated hemoglobin
D: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7568
Polymers51,2904
Non-polymers2,4664
Water9,602533
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.380, 105.050, 151.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain "A"
21chain "B"
31chain "C"
41chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
111SERALAA1 - 116
121HEMHEMB
211SERALAC1 - 116
221HEMHEMD
311SERALAE1 - 116
321HEMHEMF
411SERALAG1 - 116
421HEMHEMH

NCS oper:
IDCodeMatrixVector
1given(0.999971630002, 0.00718019812673, -0.00227682801654), (0.00723349592767, -0.999677687608, 0.0243351070463), (-0.00210136327663, -0.0243508860856, -0.999701264688)-0.308297926561, 95.8798002612, 41.0900266894
2given(-0.999991953968, -0.0039084791176, -0.000903211205434), (0.000969296245203, -0.0169393918992, -0.999856048372), (0.0038926166371, -0.999848878978, 0.0169430440785)5.54120247209, 69.029062653, 67.7692405068
3given(-0.999955214202, 0.00208820757469, -0.00923087097112), (-0.00921962163012, 0.0053340468561, 0.999943271652), (0.0021373270124, 0.999983593532, -0.00531455548284)5.42960543887, 28.1653730535, -28.2458937699

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Components

#1: Protein
Group 1 truncated hemoglobin


Mass: 12822.427 Da / Num. of mol.: 4 / Mutation: C51S, C71S, Y34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris, pH 6.5, 28% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Sep 16, 2021
RadiationMonochromator: MIrror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→24.28 Å / Num. obs: 30655 / % possible obs: 99.98 % / Redundancy: 3.04 % / Biso Wilson estimate: 11.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 5684 / CC1/2: 0.981 / Rpim(I) all: 0.091 / Rrim(I) all: 0.146 / % possible all: 99.84

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Processing

Software
NameVersionClassification
CrysalisPro1.171.41.93adata reduction
CrysalisPro1.171.41.93adata scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
Coot0.9.5model building
RefinementMethod to determine structure: SAD
Starting model: PDB entry 3AQ7

3aq7


Resolution: 2→23.45 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.41
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: MR-SAD: rough MR solution combined with purely SAD-based structure factors obtained from anomalous data
RfactorNum. reflection% reflection
Rfree0.2026 1983 6.53 %
Rwork0.1748 28405 -
obs0.1766 30388 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.58 Å2
Refinement stepCycle: LAST / Resolution: 2→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 172 533 4293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373832
X-RAY DIFFRACTIONf_angle_d0.53925216
X-RAY DIFFRACTIONf_chiral_restr0.0391548
X-RAY DIFFRACTIONf_plane_restr0.0038672
X-RAY DIFFRACTIONf_dihedral_angle_d15.71641416
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
12AX-RAY DIFFRACTIONTorsion NCS0.482315241447
13AX-RAY DIFFRACTIONTorsion NCS0.55916810492
14AX-RAY DIFFRACTIONTorsion NCS0.590211500961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.22761400.18291950X-RAY DIFFRACTION98
2.05-2.110.27671410.18022021X-RAY DIFFRACTION99
2.11-2.170.20461340.17521947X-RAY DIFFRACTION99
2.17-2.240.21561360.17271984X-RAY DIFFRACTION99
2.24-2.320.20211410.172005X-RAY DIFFRACTION99
2.32-2.410.20071380.1741969X-RAY DIFFRACTION99
2.41-2.520.20211420.1762042X-RAY DIFFRACTION99
2.52-2.650.2671370.17811981X-RAY DIFFRACTION99
2.65-2.820.23951400.18922029X-RAY DIFFRACTION99
2.82-3.040.20221430.18312054X-RAY DIFFRACTION100
3.04-3.340.17031420.18722023X-RAY DIFFRACTION100
3.34-3.820.19591460.16332081X-RAY DIFFRACTION100
3.82-4.810.16861470.15232089X-RAY DIFFRACTION100
4.81-23.450.18121560.18182230X-RAY DIFFRACTION100

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