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- PDB-5jab: Structure of the biliverdin reductase Rv2074 from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5jab
TitleStructure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex with F420
ComponentsBiliverdin reductase Rv2074
KeywordsOXIDOREDUCTASE / biliverdin reductase / split beta-barrel fold / flavin/deazaflavin oxidoreductase / F420 binding protein
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With other, known, physiological acceptors / coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / peptidoglycan-based cell wall / cell surface / protein homodimerization activity / extracellular region
Similarity search - Function
F420-binding domain, putative / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
COENZYME F420-3 / F420H(2)-dependent biliverdin reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsAhmed, F.H. / Carr, P.D. / Jackson, C.J.
CitationJournal: Protein Sci. / Year: 2016
Title: Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis.
Authors: Ahmed, F.H. / Mohamed, A.E. / Carr, P.D. / Lee, B.M. / Condic-Jurkic, K. / O'Mara, M.L. / Jackson, C.J.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biliverdin reductase Rv2074
B: Biliverdin reductase Rv2074
C: Biliverdin reductase Rv2074
D: Biliverdin reductase Rv2074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,02012
Polymers59,2674
Non-polymers3,7538
Water11,782654
1
A: Biliverdin reductase Rv2074
B: Biliverdin reductase Rv2074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5106
Polymers29,6342
Non-polymers1,8764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-36 kcal/mol
Surface area12870 Å2
MethodPISA
2
C: Biliverdin reductase Rv2074
D: Biliverdin reductase Rv2074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5106
Polymers29,6342
Non-polymers1,8764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-37 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.756, 88.620, 98.625
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA9 - 1349 - 134
21ARGARGLEULEUBB9 - 1349 - 134
12ARGARGLEULEUAA9 - 1349 - 134
22ARGARGLEULEUCC9 - 1349 - 134
13ALAALALEULEUAA2 - 1342 - 134
23ALAALALEULEUDD2 - 1342 - 134
14ARGARGASPASPBB9 - 1359 - 135
24ARGARGASPASPCC9 - 1359 - 135
15ARGARGLEULEUBB9 - 1349 - 134
25ARGARGLEULEUDD9 - 1349 - 134
16ARGARGLEULEUCC9 - 1349 - 134
26ARGARGLEULEUDD9 - 1349 - 134

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Biliverdin reductase Rv2074


Mass: 14816.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2074, MTCY49.13 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WLL7
#2: Chemical
ChemComp-6J4 / COENZYME F420-3


Mass: 902.707 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H43N6O21P
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 27% PEG3350, 0.2M MgCl2, 0.1 M BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→65.92 Å / Num. obs: 65830 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.181 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.686.71.261199.9
9.04-65.925.90.094198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ASF

2asf


Resolution: 1.65→65.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.29 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 3266 5 %RANDOM
Rwork0.1782 ---
obs0.1801 62534 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.08 Å2 / Biso mean: 20.763 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.65→65.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 252 654 4940
Biso mean--22.89 30.46 -
Num. residues----523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194451
X-RAY DIFFRACTIONr_bond_other_d0.010.024273
X-RAY DIFFRACTIONr_angle_refined_deg1.9622.0216078
X-RAY DIFFRACTIONr_angle_other_deg1.68239756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5565547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.05221.841201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34515708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1031564
X-RAY DIFFRACTIONr_chiral_restr0.1120.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025044
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021048
X-RAY DIFFRACTIONr_mcbond_it2.0141.7792128
X-RAY DIFFRACTIONr_mcbond_other2.0071.7772127
X-RAY DIFFRACTIONr_mcangle_it2.9242.652662
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73040.12
12B73040.12
21A74500.1
22C74500.1
31A77620.1
32D77620.1
41B75000.1
42C75000.1
51B74680.11
52D74680.11
61C74090.1
62D74090.1
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 223 -
Rwork0.295 4565 -
all-4788 -
obs--99.92 %

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