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- PDB-4nl5: Mycobacterium tuberculosis heme-degrading protein MhuD in complex... -

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Basic information

Entry
Database: PDB / ID: 4nl5
TitleMycobacterium tuberculosis heme-degrading protein MhuD in complex with heme and cyanide
ComponentsHeme-degrading monooxygenase HmoB
KeywordsOXIDOREDUCTASE / beta barrel
Function / homology
Function and homology information


heme oxygenase (mycobilin-producing) / heme oxygenase (decyclizing) activity / heme catabolic process / cell wall / peptidoglycan-based cell wall / heme binding / metal ion binding / plasma membrane
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase (mycobilin-producing) / Heme oxygenase (mycobilin-producing)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMorse, R.P. / Chao, A. / Goulding, C.W.
CitationJournal: Inorg.Chem. / Year: 2014
Title: Crystallographic and Spectroscopic Insights into Heme Degradation by Mycobacterium tuberculosis MhuD.
Authors: Graves, A.B. / Morse, R.P. / Chao, A. / Iniguez, A. / Goulding, C.W. / Liptak, M.D.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Heme-degrading monooxygenase HmoB
B: Heme-degrading monooxygenase HmoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7898
Polymers26,3862
Non-polymers1,4036
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-64 kcal/mol
Surface area9770 Å2
MethodPISA
2
A: Heme-degrading monooxygenase HmoB
hetero molecules

B: Heme-degrading monooxygenase HmoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7898
Polymers26,3862
Non-polymers1,4036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area4570 Å2
ΔGint-57 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.970, 60.400, 78.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme-degrading monooxygenase HmoB / Heme oxygenase / Mycobacterial heme utilization degrader / MHUD


Mass: 13192.880 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: mhuD, MT3698, Rv3592 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: O06156, UniProt: P9WKH3*PLUS, heme oxygenase (biliverdin-producing)
#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-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.84 Å3/Da / Density % sol: 33.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.9 M Ammonium Sulfate, 0.1 M Sodium Acetate, pH 6.0, 0.2 M Sodium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→39.23 Å / Num. all: 103418 / Num. obs: 15989 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.23 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1595 10.01 %Random
Rwork0.173 ---
obs0.1782 15935 99.94 %-
all-110652 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 98 94 1697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011661
X-RAY DIFFRACTIONf_angle_d1.0982282
X-RAY DIFFRACTIONf_dihedral_angle_d14.834546
X-RAY DIFFRACTIONf_chiral_restr0.044227
X-RAY DIFFRACTIONf_plane_restr0.006296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96140.24441440.19581287X-RAY DIFFRACTION100
1.9614-2.03150.25271410.18371273X-RAY DIFFRACTION100
2.0315-2.11280.24291410.18351269X-RAY DIFFRACTION100
2.1128-2.2090.23871440.18461291X-RAY DIFFRACTION100
2.209-2.32540.26041430.17661290X-RAY DIFFRACTION100
2.3254-2.47110.26111420.18311279X-RAY DIFFRACTION100
2.4711-2.66180.21131430.19181291X-RAY DIFFRACTION100
2.6618-2.92960.23321460.18911314X-RAY DIFFRACTION100
2.9296-3.35330.2471450.18271308X-RAY DIFFRACTION100
3.3533-4.22410.20631480.15771325X-RAY DIFFRACTION100
4.2241-39.23830.19011580.15311413X-RAY DIFFRACTION100
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)
18.70980.5952-4.96562.3985-0.7295.1243-0.05610.19030.1051-0.10820.0878-0.245-0.14920.2088-0.0360.13270.00280.01860.20930.03010.1591-3.8494-0.981913.2437
22.014-0.0862-1.69555.90892.54518.56980.38080.7509-1.04130.31360.5336-0.61480.66970.6803-0.89970.22910.0961-0.09360.3819-0.07620.40575.1065-10.638913.4399
36.54052.6597-5.2572.6101-1.0475.7192-0.1482-0.3121-0.92630.3876-0.1667-0.41620.80820.210.30820.2871-0.00970.00130.20850.0460.3368-8.4445-12.930617.5306
46.54-4.17930.37899.55783.30767.933-0.15360.37840.2159-0.1615-0.0342-0.0957-0.31490.64620.20640.1504-0.02830.00940.24720.03990.2105-0.80660.78243.4669
51.8622-1.84331.17994.69141.99224.1674-0.2679-0.3468-0.34950.09880.05670.28540.4866-0.00180.2020.12490.0370.02740.1670.03270.144-11.0166-5.893114.5421
66.19670.53373.59757.3173-4.82462.01040.0378-0.81420.2240.8285-0.08250.109-0.9579-0.2620.03930.35720.02050.0380.37130.00780.1431-14.5277-4.261724.8542
79.58390.7016-6.39753.7701-3.16092.0145-0.2325-1.2713-0.0515-0.04640.1331-0.05550.34140.64050.0840.23030.0016-0.02290.39890.0110.1969-4.9608-6.958427.843
89.15679.3341-7.78741.9981-6.92287.6234-1.0195-1.1274-0.6740.35721.0546-0.9020.67050.4019-0.25410.51480.1039-0.02940.7281-0.01390.40067.187-5.232721.6918
92.00212.92957.82253.03721.89715.52620.0352-0.66640.15730.1831-0.1260.1762-0.1846-0.27810.05070.23050.04950.02120.2629-0.01840.1698-11.27632.728915.502
106.6306-5.1491-3.77525.49261.9047.195-0.12940.3225-1.1202-0.17080.04330.50570.857-0.91220.06380.2235-0.09880.01180.3498-0.03020.4413-22.2213-7.56953.8269
118.8815-7.4312-2.80989.80624.39416.50010.18240.13090.1965-0.2064-0.268-0.0752-0.3748-0.10670.06520.08110.0010.01730.183-0.03340.1776-12.30791.41151.0529
124.1176-1.8745-3.84239.32181.81485.9587-0.1760.0080.0805-0.01050.05490.6882-0.3173-0.88320.14530.15920.0798-0.02640.3319-0.00890.1852-27.29616.96863.0517
136.4039-8.86-5.70082.02917.82055.2087-0.14320.3982-0.61390.312-0.66510.83970.5733-1.01610.72490.3767-0.15390.01880.4527-0.04240.4476-23.2598-7.3981-6.519
142.6964-3.4617-2.98579.37069.92042.0485-0.0003-0.0146-0.47870.3933-0.63120.68190.2341-1.01320.65350.25260.00550.03670.25890.00920.2622-18.2233-5.95072.0808
157.9051-3.0467-0.4914.5719-2.38088.2714-0.1138-0.61030.0960.2746-0.0883-0.2536-1.1168-0.46860.22290.25530.02810.03820.2349-0.05060.1756-15.79867.361412.1061
168.9022-3.6354-3.35465.36574.30678.41930.00480.0372-0.62360.022-0.18020.16050.3288-0.14430.14350.1177-0.00490.02970.15820.01240.1318-13.8031-4.33250.8164
172.0423-6.99097.21449.6981-6.58388.84280.44521.0440.0095-0.6012-0.4829-0.2610.15940.54920.02990.2652-0.02710.00640.2553-0.04340.2139-14.065-3.2145-10.854
180.0737-0.9053-0.78122.00019.55958.4085-0.00140.34710.1651-0.3521-0.69931.3272-0.6625-1.84210.66990.63390.1071-0.09640.74250.11050.4313-27.36159.4624-7.3005
193.0701-3.07191.98459.0075-3.81145.11870.20590.1462-0.1364-0.0861-0.18710.19050.10090.041-0.03340.0948-0.03010.0060.1365-0.03250.1208-8.4141-3.88954.2604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 59 )
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 67 )
7X-RAY DIFFRACTION7chain 'A' and (resid 68 through 75 )
8X-RAY DIFFRACTION8chain 'A' and (resid 76 through 85 )
9X-RAY DIFFRACTION9chain 'A' and (resid 86 through 93 )
10X-RAY DIFFRACTION10chain 'A' and (resid 94 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 11 )
12X-RAY DIFFRACTION12chain 'B' and (resid 12 through 25 )
13X-RAY DIFFRACTION13chain 'B' and (resid 26 through 35 )
14X-RAY DIFFRACTION14chain 'B' and (resid 36 through 42 )
15X-RAY DIFFRACTION15chain 'B' and (resid 43 through 50 )
16X-RAY DIFFRACTION16chain 'B' and (resid 51 through 59 )
17X-RAY DIFFRACTION17chain 'B' and (resid 60 through 75 )
18X-RAY DIFFRACTION18chain 'B' and (resid 76 through 83 )
19X-RAY DIFFRACTION19chain 'B' and (resid 84 through 101 )

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