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- PDB-3tld: Crystal Structure of Y29F mutant of Vitreoscilla hemoglobin -

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Basic information

Entry
Database: PDB / ID: 3tld
TitleCrystal Structure of Y29F mutant of Vitreoscilla hemoglobin
ComponentsBacterial hemoglobin
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: 1.896 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 29, 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 / 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_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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Bacterial hemoglobin
B: Bacterial hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0587
Polymers31,5492
Non-polymers1,5095
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-59 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.614, 41.068, 62.395
Angle α, β, γ (deg.)90.000, 105.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterial hemoglobin / Soluble cytochrome O


Mass: 15774.269 Da / Num. of mol.: 2 / Mutation: Y29F
Source method: isolated from a genetically manipulated source
Details: Cloned in pET-28c (+) (Novagen) at the NdeI and BamHI sites
Source: (gene. exp.) Vitreoscilla stercoraria (bacteria) / Gene: vhb / Plasmid: pY29F / Production host: Escherichia coli (E. coli) / Strain (production host): pET-28c / References: UniProt: P04252
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30 mg/mL protein in 1.2M (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: Aug 12, 2009
Details: Si(111) monochromator with sagittally bent second crystal
RadiationMonochromator: Si 111 - sagittal 2nd crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→31.5 Å / Num. all: 27232 / Num. obs: 27232 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.0593 / Rsym value: 0.0593 / Net I/σ(I): 16.44
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.77-1.83331.490.23823.290.2382161.7
1.9935-2.09853.70.13097.310.13091100
3.81-313.370.04535.10.045198.7

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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: 1.896→31.575 Å / FOM work R set: 0.8945 / SU ML: 0.14 / σ(F): 0 / Phase error: 17.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1888 1998 8.47 %
Rwork0.1647 21593 -
obs0.1668 23591 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.81 Å2 / Biso mean: 26.84 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: LAST / Resolution: 1.896→31.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 104 241 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052362
X-RAY DIFFRACTIONf_angle_d1.0813241
X-RAY DIFFRACTIONf_chiral_restr0.034374
X-RAY DIFFRACTIONf_plane_restr0.005404
X-RAY DIFFRACTIONf_dihedral_angle_d14.804833
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 (%)
1.896-1.94340.20241060.19991224133078
1.9434-1.9960.21171320.18841433156592
1.996-2.05470.21281480.177415681716100
2.0547-2.1210.19181410.173515441685100
2.121-2.19680.18181500.15715821732100
2.1968-2.28470.20581390.156515761715100
2.2847-2.38870.1651450.158515581703100
2.3887-2.51460.16481460.150315661712100
2.5146-2.6720.18951470.150415771724100
2.672-2.87820.1761470.158215821729100
2.8782-3.16760.21271450.167915781723100
3.1676-3.62540.18461480.161415811729100
3.6254-4.56540.17341540.148915941748100
4.5654-31.57940.20231500.18841630178098
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)
10.0458-0.0849-0.00720.3996-0.03810.07380.0627-0.0159-0.0876-0.0435-0.01890.3254-0.0202-0.06950.04170.14580.05480.08020.1924-0.03630.2961-11.65464.9094-23.9627
20.28250.01640.03770.0435-0.03630.04210.0193-0.12080.06430.2472-0.02160.0461-0.04720.089-0.13980.1546-0.0020.01270.1425-0.00230.05416.5281-3.4421-17.9493
30.013-0.0064-0.01020.00730.00240.00760.0608-0.1250.09120.04150.1448-0.17690.08140.1659-0.00050.17090.0515-0.00190.15870.00380.199512.0948-12.4277-24.1834
40.2007-0.22680.16450.35240.14221.19160.0750.02-0.61110.02640.0232-0.66380.46310.62350.02760.22090.0847-0.03630.27240.060.52716.6512-3.3609-26.2157
50.0930.06140.04440.3394-0.13360.11360.0057-0.10730.0230.1277-0.13610.0647-0.0639-0.2048-0.09510.07790.0189-0.00630.1521-0.04180.0757-2.11343.6827-28.6336
60.3402-0.02820.16110.6161-0.16170.50740.0232-0.17630.0685-0.18250.0454-0.09180.0141-0.15910.06090.14370.0225-0.02940.0868-0.0120.09421.0936-2.1452-37.9371
70.1186-0.05380.08330.04920.04380.3676-0.0624-0.217-0.12020.23180.04750.16120.1984-0.05240.06780.12650.00360.04530.1557-0.00360.1391-2.4694-4.9114-18.9304
80.40250.06420.15920.8771-0.16820.26050.03170.0947-0.113-0.142-0.1530.450.0761-0.17350.30380.10740.0194-0.05190.1525-0.04230.1792-4.2767-8.0168-33.3202
90.0843-0.06040.06850.1995-0.03840.0637-0.1219-0.0691-0.19180.0519-0.0808-0.10080.17190.0753-0.47210.07-0.09250.21130.15070.13780.2906-25.785-10.2723-43.2947
100.01970.01020.05020.00710.01640.2564-0.07840.1243-0.0480.0534-0.0410.24440.0026-0.1492-0.01010.0907-0.00850.00240.1662-0.010.1758-26.1462-1.406-61.8199
110.0127-0.0019-0.01180.0089-0.00180.0103-0.06890.09970.0078-0.06320.0749-0.01710.0875-0.055900.2044-0.00090.00060.15250.05270.1468-18.63147.577-65.3135
120.3234-0.06720.00930.1715-0.1730.17860.00450.4880.3476-0.5611-0.0954-0.2101-0.45940.0905-0.03270.43740.0403-0.0060.26090.06360.1922-15.3303-1.7375-69.1439
130.1411-0.1861-0.02270.28020.03010.0940.0097-0.1472-0.1328-0.0688-0.11830.08780.1674-0.1434-0.02770.1116-0.0387-0.00090.1526-0.0020.1171-18.3895-8.5534-50.4348
140.3327-0.19180.20910.60340.0290.2057-0.0868-0.0511-0.0244-0.09030.0488-0.14850.0119-0.2010.03390.1284-0.0219-0.05340.09230.01630.1327-8.6876-2.9286-50.5416
150.10660.04940.11070.1219-0.02080.2787-0.06050.03620.09960.020.03660.2414-0.1261-0.1722-0.05540.136-0.0050.03580.1577-0.01630.1593-28.0979-0.2702-52.739
160.1236-0.20050.14080.4986-0.01160.40970.0743-0.20930.00670.3018-0.1211-0.0496-0.0989-0.0202-0.34080.1928-0.0348-0.02450.14480.01370.1014-14.9393.0296-47.0523
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
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 20)B0
10X-RAY DIFFRACTION10chain 'B' and (resid 21 through 36)B0
11X-RAY DIFFRACTION11chain 'B' and (resid 37 through 43)B0
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 56)B0
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 67)B0
14X-RAY DIFFRACTION14chain 'B' and (resid 68 through 90)B0
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 115)B0
16X-RAY DIFFRACTION16chain 'B' and (resid 116 through 146)B0

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