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- PDB-3tm3: Wild-type hemoglobin from Vitreoscilla stercoraria -

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Basic information

Entry
Database: PDB / ID: 3tm3
TitleWild-type hemoglobin from Vitreoscilla stercoraria
ComponentsHemoglobin
KeywordsOXYGEN TRANSPORT / globin 8-helix fold / oxygen storage
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bacterial hemoglobin
Similarity search - Component
Biological speciesVitreoscilla stercoraria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRatakonda, S. / Anand, A. / Dikshit, K. / Stark, B.C. / Howard, A.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallographic structure determination of B10 mutants of Vitreoscilla hemoglobin: role of Tyr29 (B10) in the structure of the ligand-binding site.
Authors: Ratakonda, S. / Anand, A. / Dikshit, K. / Stark, B.C. / Howard, A.J.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4072
Polymers15,7901
Non-polymers6161
Water1,65792
1
A: Hemoglobin
hetero molecules

A: Hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8144
Polymers31,5812
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+5/21
Buried area3530 Å2
ΔGint-54 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.156, 99.013, 41.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-371-

HOH

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Components

#1: Protein Hemoglobin / / Soluble cytochrome O


Mass: 15790.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cloned into pBluescript 11KS+ at its SmaI site; see Dikshit et al. (1998) Arch Biochem Biophys 349:161.
Source: (gene. exp.) Vitreoscilla stercoraria (bacteria) / Gene: vhb / Plasmid: PDH88 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P04252
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25 mg/mL protein in 1.6M (NH4)2SO4, 0.05M NaH2P2O7, 3% ethylene glycol, streak-seeded, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 6, 2010
Details: Si(111) monochromator with sagittally bent second crystal
RadiationMonochromator: Si111 - sagittal second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30.2 Å / Num. all: 32704 / Num. obs: 32704 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.05 % / Biso Wilson estimate: 50.05 Å2 / Rmerge(I) obs: 0.0548 / Rsym value: 0.0548 / Net I/σ(I): 10.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.7-1.7613.040.52881.23732890.5288100
1.761-1.8313.050.4331.62632550.433100
3.6625-32.12.870.026531.732340.026594.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.932 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 1575 9.98 %
Rwork0.1703 14199 -
obs0.1737 15774 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.92 Å2 / Biso mean: 34.6799 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 43 92 1225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051186
X-RAY DIFFRACTIONf_angle_d1.0871628
X-RAY DIFFRACTIONf_chiral_restr0.032190
X-RAY DIFFRACTIONf_plane_restr0.005201
X-RAY DIFFRACTIONf_dihedral_angle_d14.44424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.80660.31511400.26441252139299
1.8066-1.87110.31051410.227912921433100
1.8711-1.94610.19951380.19881264140299
1.9461-2.03460.21721400.186612531393100
2.0346-2.14180.22811440.170412971441100
2.1418-2.2760.19981410.158812701411100
2.276-2.45160.19021420.156612771419100
2.4516-2.69820.16721460.151913091455100
2.6982-3.08830.18321440.158412961440100
3.0883-3.88960.171470.160713191466100
3.8896-29.93620.22411520.17071370152299
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)
10.1179-0.0872-0.16170.146-0.02020.4896-0.2640.0603-0.1613-0.1286-0.00480.02490.4706-0.0552-0.73250.573-0.00470.11450.07670.15160.274586.9564.988358.8293
20.0095-0.01580.01340.0176-0.02870.0279-0.07320.09390.0319-0.05430.0497-0.25890.27430.070.00020.17490.04830.02190.17060.02270.2341102.685816.049750.3327
30.00430.0117-0.0060.0284-0.01890.0192-0.0063-0.02340.26390.1123-0.2011-0.3071-0.15780.204-0.00040.18790.01180.0090.2510.03540.244100.831824.243141.3948
4-0.00240.0018-0.0003-0.0016-0.0039-0.0010.18110.25140.4157-0.34230.3992-0.234-0.56960.07320.0150.4273-0.19220.09720.56020.10550.5217102.765929.189149.7599
50.0266-0.0174-0.01140.05410.03020.01980.123-0.0677-0.19120.43190.0648-0.0244-0.07660.13060.00050.18010.0017-0.0150.1620.02380.213289.101315.91957.4382
60.0999-0.119-0.13830.1280.12110.1633-0.09140.1169-0.23960.1350.03940.0567-0.1308-0.2912-0.00070.16170.0410.020.28890.01950.168983.257323.584351.5815
70.11430.07-0.05270.10260.04020.1044-0.13120.1424-0.2676-0.2517-0.0171-0.20520.25170.0661-0.00570.2407-0.00960.04670.16640.00760.238996.81049.674648.78
80.13430.0605-0.43810.0252-0.19341.487-0.09820.1107-0.1339-0.16220.2580.30630.4376-0.7596-0.03550.188-0.123-0.00380.22940.04980.210584.221315.860446.1278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 36 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 43)A0
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 55)A0
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 67)A0
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 90)A0
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 114)A0
8X-RAY DIFFRACTION8chain 'A' and (resid 115 through 146)A0

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