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- PDB-6wk3: Engineered carbene transferase RmaNOD Q52V, putative nitric oxide... -

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Basic information

Entry
Database: PDB / ID: 6wk3
TitleEngineered carbene transferase RmaNOD Q52V, putative nitric oxide dioxygenase from Rhodothermus marinus
ComponentsNitric oxide dioxygenase
KeywordsMETAL BINDING PROTEIN / Heme binding protein / Carbene transferase / Globin
Function / homology
Function and homology information


nitric oxide dioxygenase / nitric oxide dioxygenase NAD(P)H activity / response to nitrosative stress / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Flavohemoprotein / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide dioxygenase
Similarity search - Component
Biological speciesRhodothermus marinus DSM 4252 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsKnight, A.M. / Arnold, F.H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1513007 United States
National Science Foundation (NSF, United States)STTR-1549855 United States
National Science Foundation (NSF, United States)DGE-1144469 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-07616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-112592 United States
CitationJournal: Acs Catalysis / Year: 2020
Title: Diversity-Oriented Enzymatic Synthesis of Cyclopropane Building Blocks.
Authors: Wittmann, B.J. / Knight, A.M. / Hofstra, J.L. / Reisman, S.E. / Kan, S.B.J. / Arnold, F.H.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_conn.ptnr2_symmetry
Revision 1.2Mar 6, 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: Nitric oxide dioxygenase
B: Nitric oxide dioxygenase
C: Nitric oxide dioxygenase
D: Nitric oxide dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,71019
Polymers65,5684
Non-polymers3,14215
Water181
1
A: Nitric oxide dioxygenase
B: Nitric oxide dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3219
Polymers32,7842
Non-polymers1,5377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area14830 Å2
MethodPISA
2
C: Nitric oxide dioxygenase
hetero molecules

D: Nitric oxide dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,38910
Polymers32,7842
Non-polymers1,6058
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area1970 Å2
ΔGint-5 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.269, 102.472, 84.273
Angle α, β, γ (deg.)90.000, 98.529, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Nitric oxide dioxygenase /


Mass: 16391.928 Da / Num. of mol.: 4 / Mutation: Q52V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus DSM 4252 (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / Gene: Rmar_2776 / Plasmid: pSUMO_RmaNOD_Q52V
Details (production host): pET22b encoding RmaNOD Q52V with N-terminal His-SUMO tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0MGT2, nitric oxide dioxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 40 mM Cu(II)SO4, 0.1M HEPES pH 7.6, 1.2 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.74035 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74035 Å / Relative weight: 1
ReflectionResolution: 2.45→43.65 Å / Num. obs: 36944 / % possible obs: 95.98 % / Redundancy: 6.7 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.064 / Rrim(I) all: 0.123 / Net I/σ(I): 11.7
Reflection shellResolution: 2.45→2.538 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3602 / CC1/2: 0.717 / Rpim(I) all: 0.79 / Rrim(I) all: 1.462 / % possible all: 94.17

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.45→41.67 Å / SU ML: 0.3288 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 1816 4.92 %
Rwork0.2077 35112 -
obs0.2096 36928 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.86 Å2
Refinement stepCycle: LAST / Resolution: 2.45→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4481 0 198 1 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434791
X-RAY DIFFRACTIONf_angle_d0.73486584
X-RAY DIFFRACTIONf_chiral_restr0.0367745
X-RAY DIFFRACTIONf_plane_restr0.0047814
X-RAY DIFFRACTIONf_dihedral_angle_d16.8272670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.520.31971310.29782654X-RAY DIFFRACTION94.25
2.52-2.590.36481600.28372608X-RAY DIFFRACTION94.41
2.59-2.670.29251550.27452660X-RAY DIFFRACTION94.97
2.67-2.770.33221440.27322625X-RAY DIFFRACTION94.51
2.77-2.880.32211210.26422678X-RAY DIFFRACTION94.47
2.88-3.010.31491400.26012665X-RAY DIFFRACTION95.73
3.01-3.170.30721380.25362685X-RAY DIFFRACTION95.96
3.17-3.370.26041430.25232720X-RAY DIFFRACTION96.56
3.37-3.630.26031390.21952701X-RAY DIFFRACTION96.34
3.63-3.990.23691270.19962759X-RAY DIFFRACTION97.6
3.99-4.570.2281370.17652775X-RAY DIFFRACTION97.72
4.57-5.750.22091640.20262737X-RAY DIFFRACTION97.35
5.76-41.670.18851170.15972845X-RAY DIFFRACTION98.08
Refinement TLS params.Method: refined / Origin x: 8.07758944232 Å / Origin y: 16.3263764547 Å / Origin z: 33.3602071872 Å
111213212223313233
T0.432469199414 Å20.0090182011569 Å20.00928890146978 Å2-0.411628433373 Å20.0258303636211 Å2--0.429794352643 Å2
L0.497107255816 °20.00332134339843 °2-0.0360066068485 °2-0.247072593173 °20.004256219083 °2--0.250072179154 °2
S-0.0445546507521 Å °0.0130324078922 Å °0.105999788599 Å °0.0237856807367 Å °0.0192772897079 Å °-0.0409498072128 Å °0.0158876211181 Å °0.0012390807867 Å °0.0109222683299 Å °
Refinement TLS groupSelection details: all

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