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- PDB-3tm9: Y29A mutant of Vitreoscilla stercoraria hemoglobin -

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Basic information

Entry
Database: PDB / ID: 3tm9
TitleY29A mutant of Vitreoscilla stercoraria hemoglobin
ComponentsBacterial hemoglobin
KeywordsOXYGEN TRANSPORT / globin 8-helix fold / oxygen storage
Function / homology
Function and homology information


nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin domain 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: 1.72 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 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Bacterial hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,05914
Polymers15,6981
Non-polymers1,36113
Water2,054114
1
A: Bacterial hemoglobin
hetero molecules

A: Bacterial hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,11928
Polymers31,3962
Non-polymers2,72326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5950 Å2
ΔGint-64 kcal/mol
Surface area14650 Å2
Unit cell
Length a, b, c (Å)85.194, 46.426, 62.873
Angle α, β, γ (deg.)90.000, 128.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacterial hemoglobin / Soluble cytochrome O


Mass: 15698.171 Da / Num. of mol.: 1 / Mutation: Y29A
Source method: isolated from a genetically manipulated source
Details: Tyr29Ala mutant gene was cloned into the SmaI site of pBluescript 11KS+ under control of the native vgb gene promoter.
Source: (gene. exp.) Vitreoscilla stercoraria (bacteria) / Gene: vhb / Plasmid: PDH88 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P04252
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 27 mg/mL protein in 1.3M (NH4)2SO4, 0.05M NaH2P2O7, 3% ethylene glycol. Not streak-seeded, pH 6.2, 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: Aug 12, 2009
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: 1.8→32.5 Å / Num. obs: 20497 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 41.13 Å2 / Rmerge(I) obs: 0.0707 / Rsym value: 0.0707 / Net I/σ(I): 11.002
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.8-1.8641.670.45371.690.4537147.8
1.864-1.9392.190.37942.090.3794161.9
3.878-32.53.580.031229.440.0312198

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PHASERphasing
REFMAC5.5.0109refinement
X-GENdata reduction
X-GENdata scaling
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→31.123 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 1984 9.76 %
Rwork0.1723 18349 -
obs0.1756 20333 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 25.1251 Å2 / Biso min: 9.37 Å2
Refinement stepCycle: LAST / Resolution: 1.72→31.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 91 114 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181270
X-RAY DIFFRACTIONf_angle_d1.4811719
X-RAY DIFFRACTIONf_chiral_restr0.056197
X-RAY DIFFRACTIONf_plane_restr0.009212
X-RAY DIFFRACTIONf_dihedral_angle_d16.956469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7198-1.76280.32491430.25421260140397
1.7628-1.81050.28311350.23561322145798
1.8105-1.86380.24861380.23411279141798
1.8638-1.92390.26191380.20361262140099
1.9239-1.99270.2011480.19171304145299
1.9927-2.07240.21941350.1751298143399
2.0724-2.16670.21131440.161413321476100
2.1667-2.28090.17671420.145713001442100
2.2809-2.42380.17121410.143113191460100
2.4238-2.61080.18311370.148513251462100
2.6108-2.87340.1831490.149513181467100
2.8734-3.28880.20871440.172513281472100
3.2888-4.1420.18791390.163113301469100
4.142-31.12780.21371510.182613721523100
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)
10.0543-0.08990.0030.2546-0.16080.19810.0079-0.0838-0.0543-0.0269-0.1534-0.02890.14710.0728-0.05590.13710.00050.0210.1879-0.00680.1341-7.5154-28.383712.7403
20.2129-0.10890.15250.2187-0.03370.1151-0.0846-0.2026-0.08360.16290.21790.0136-0.2163-0.55110.01810.15990.06170.00750.17350.00220.1091-24.1881-15.266812.3319
30.0431-0.04530.00420.03940.0060.0199-0.0356-0.2038-0.09210.00480.22810.084-0.1046-0.05990.00190.18240.02450.02260.144-0.01360.199-25.5589-6.1714.2055
40.0129-0.0024-0.00970.0011-0.01040.02160.1152-0.14410.1142-0.3128-0.0590.36340.0154-0.1694-0.00050.20070.0452-0.090.20530.00720.2638-31.5663-15.9133.3862
50.02870.0207-0.02280.0195-0.00450.010.0885-0.1098-0.0913-0.16340.0030.0163-0.03980.0060.00020.13170.00360.02210.13390.00790.1294-14.9758-24.94614.8935
60.32340.2051-0.20890.5791-0.0480.3835-0.21320.2804-0.1323-0.17530.4414-0.1935-0.1384-0.30630.11350.10430.1367-0.02240.03830.10530.1606-13.019-19.4831-5.4278
70.2068-0.0477-0.04820.13860.05910.2325-0.0614-0.24470.08420.063-0.0051-0.1625-0.2578-0.242-0.00990.16160.0327-0.0050.09680.00940.1018-15.28-15.36113.9878
80.1599-0.0982-0.03310.12560.06370.05430.0324-0.02340.0113-0.0015-0.1332-0.0922-0.1860.2351-0.00980.1231-0.00780.00170.13270.03740.1465-8.0095-14.4531.6259
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 56)A0
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 67)A0
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 90)A0
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 115)A0
8X-RAY DIFFRACTION8chain 'A' and (resid 116 through 146)A0

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