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- PDB-3wfw: Crystal Structure of the Closed Form of the HGbRL's Globin Domain -

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Basic information

Entry
Database: PDB / ID: 3wfw
TitleCrystal Structure of the Closed Form of the HGbRL's Globin Domain
ComponentsHemoglobin-like flavoprotein fused to Roadblock/LC7 domain
KeywordsOXYGEN TRANSPORT / Globin / Signalling / Closed form
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 / Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
Similarity search - Component
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTeh, A.H.
CitationJournal: Sci Rep / Year: 2015
Title: Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites.
Authors: Teh, A.H. / Saito, J.A. / Najimudin, N. / Alam, M.
History
DepositionJul 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Derived calculations / Category: citation / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4154
Polymers16,5621
Non-polymers8533
Water2,342130
1
A: Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
hetero molecules

A: Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8308
Polymers33,1252
Non-polymers1,7066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9230 Å2
ΔGint-155 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.240, 54.400, 44.710
Angle α, β, γ (deg.)90.00, 106.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21A-355-

HOH

31A-394-

HOH

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Components

#1: Protein Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain


Mass: 16562.338 Da / Num. of mol.: 1 / Fragment: N-terminal Globin Domain, UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum infernorum (bacteria)
Strain: V4 / Gene: hmp, Minf_1089 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / References: UniProt: B3DUZ1
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl, 0.2M (NH4)2HPO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 23, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 38021 / % possible obs: 89.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 14.37 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 22.01
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 10.96 / Num. unique all: 1192 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX1.8.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.514 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.11 / σ(F): 2 / Phase error: 17.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 841 5 %Random
Rwork0.151 ---
all0.1519 16812 --
obs0.1519 16812 89.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.65 Å2 / Biso mean: 19.6599 Å2 / Biso min: 7.4 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 59 130 1355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091339
X-RAY DIFFRACTIONf_angle_d1.2011839
X-RAY DIFFRACTIONf_dihedral_angle_d16.882517
X-RAY DIFFRACTIONf_chiral_restr0.079189
X-RAY DIFFRACTIONf_plane_restr0.006224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.75340.16191350.14622566270187
1.7534-1.88880.20191390.15032635277489
1.8888-2.07880.17311380.15122619275789
2.0788-2.37940.18221410.14352680282190
2.3794-2.99720.16581400.16142676281690
2.9972-27.51820.15821480.14932795294392
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)
12.24421.27411.17329.0719-4.03355.7037-0.39450.6450.1695-0.46980.35810.43770.1481-0.53520.04690.1315-0.02340.0070.2292-0.01850.125923.552-3.713632.9065
23.28023.23263.48936.6014.87374.3575-0.1738-0.44290.53280.47810.1239-0.2997-0.08060.10320.00870.17930.01370.01080.13330.01480.164616.0772-2.417931.4978
34.50912.49933.54193.5045-1.06598.20.3087-0.6599-0.3930.19210.05270.45940.4419-0.7632-0.26970.168-0.00850.01710.17250.02950.14525.6891-4.575728.7587
45.95690.53960.10966.7849-5.29314.2931-0.0962-0.146-0.44210.09020.16120.206-0.0243-0.4809-0.08780.08210.01170.00410.1404-0.01920.1491-0.5506-2.161621.6397
57.1137-1.0081-0.98677.72041.81858.59910.04610.46760.2779-0.2516-0.00550.0223-0.33820.0081-0.04710.0942-0.0129-0.02310.08750.02050.10612.43545.557711.2292
67.6616-1.34733.48619.73532.49375.8402-0.07330.21410.1469-0.3951-0.1152-0.3803-0.3277-0.08550.20830.1226-0.0002-0.01330.22690.02270.08483.3692.7932.6544
77.93314.91833.07953.15851.20047.92340.00030.4264-0.84910.04450.06540.0530.4691-0.5583-0.03290.1295-0.0169-0.02360.2148-0.01410.2353-2.7828-5.01747.9892
88.99214.60464.84495.72484.33238.4240.118-0.1944-0.3610.0911-0.02170.46460.2062-0.4639-0.09390.1067-0.00360.00030.08650.0140.16135.7499-6.14616.3322
98.3643-1.5095.91976.4819-0.97555.75510.02880.44820.2114-0.3923-0.0427-0.08320.1220.2699-0.01140.1427-0.01640.02130.06890.00410.098917.0499-8.276119.6716
104.85911.74046.79872.42131.87449.67330.3281-0.2497-0.97130.05660.10560.01770.2206-0.2429-0.43540.1378-0.0150.01040.11160.03780.19326.6094-10.722428.2644
116.29780.05160.4516.3195-3.93788.11940.0677-0.6378-0.6978-0.0771-0.0627-0.14030.325-0.39050.03210.1173-0.02510.01350.15990.05860.156635.7581-10.396736.4211
128.1329-5.118-2.10268.05081.98867.2884-0.0891-0.7331-0.02270.18030.142-0.37410.01820.133-0.03110.10290.0113-0.00070.27380.01780.092641.7335-4.466240.876
135.28823.16491.14067.765-5.2016.5499-0.0726-0.46930.29660.28740.19750.0328-0.34390.1074-0.10950.12470.03530.01010.1368-0.06380.164341.00654.446736.2003
145.59313.4504-0.72365.4295-4.88568.27790.087-0.08710.64350.0366-0.05280.2843-0.2579-0.0788-0.05450.1046-0.0008-0.00840.0504-0.00170.165845.45396.360826.1528
152.6865-2.9746-1.54127.3517-3.5057.697-0.17640.36690.1823-0.3694-0.0841-0.2165-0.07190.49520.22470.135-0.0363-0.02510.090.02970.168849.56956.443818.8669
169.4707-0.6936-2.12372.9957-2.38842.68740.40971.66130.4441-0.8867-0.55810.0078-0.17990.26270.15740.23340.0350.00210.32230.06750.216647.14716.669312.0012
172.02051.4951-1.58084.7938-4.30993.8504-0.0163-0.07320.150.00350.1548-0.0453-0.17410.1852-0.15810.1399-0.0102-0.01280.08130.00110.165637.58376.14316.9287
186.78624.8361-3.7133.6624-3.72458.94160.0316-0.02640.23970.06420.16060.0853-0.2285-0.1929-0.15520.10080.015800.05270.00450.125833.99060.342829.6498
199.33151.04624.88796.0236-2.29483.96420.2025-1.0768-0.25150.1092-0.16520.0089-0.0483-0.4816-0.00810.1473-0.00230.00370.2613-0.00220.146331.9684-1.95339.274
202.0012.11629.82956.72242.47089.6853-0.6947-0.0147-0.1861-0.4291-0.56260.0563-0.6976-0.52381.05440.52370.01860.19330.5303-0.06610.283432.9491-3.531646.6055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:4)A1 - 4
2X-RAY DIFFRACTION2(chain A and resid 5:12)A5 - 12
3X-RAY DIFFRACTION3(chain A and resid 13:18)A13 - 18
4X-RAY DIFFRACTION4(chain A and resid 19:26)A19 - 26
5X-RAY DIFFRACTION5(chain A and resid 27:35)A27 - 35
6X-RAY DIFFRACTION6(chain A and resid 36:41)A36 - 41
7X-RAY DIFFRACTION7(chain A and resid 42:48)A42 - 48
8X-RAY DIFFRACTION8(chain A and resid 49:57)A49 - 57
9X-RAY DIFFRACTION9(chain A and resid 58:64)A58 - 64
10X-RAY DIFFRACTION10(chain A and resid 65:74)A65 - 74
11X-RAY DIFFRACTION11(chain A and resid 75:80)A75 - 80
12X-RAY DIFFRACTION12(chain A and resid 81:88)A81 - 88
13X-RAY DIFFRACTION13(chain A and resid 89:93)A89 - 93
14X-RAY DIFFRACTION14(chain A and resid 94:100)A94 - 100
15X-RAY DIFFRACTION15(chain A and resid 101:105)A101 - 105
16X-RAY DIFFRACTION16(chain A and resid 106:110)A106 - 110
17X-RAY DIFFRACTION17(chain A and resid 111:120)A111 - 120
18X-RAY DIFFRACTION18(chain A and resid 121:129)A121 - 129
19X-RAY DIFFRACTION19(chain A and resid 130:134)A130 - 134
20X-RAY DIFFRACTION20(chain A and resid 135:138)A135 - 138

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