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- PDB-3k9z: Rational Design of a Structural and Functional Nitric Oxide Reductase -

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Basic information

Entry
Database: PDB / ID: 3k9z
TitleRational Design of a Structural and Functional Nitric Oxide Reductase
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Alpha HELIX / Heme / Iron / Metal-binding / Nitric Oxide Reduction
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.72 Å
AuthorsYeung, N. / Lin, Y.-W. / Gao, Y.-G. / Zhao, X. / Russell, B.S. / Lei, L. / Miner, K.D. / Robinson, H. / Lu, Y.
CitationJournal: Nature / Year: 2009
Title: Rational design of a structural and functional nitric oxide reductase.
Authors: Yeung, N. / Lin, Y.W. / Gao, Y.G. / Zhao, X. / Russell, B.S. / Lei, L. / Miner, K.D. / Robinson, H. / Lu, Y.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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.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_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_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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9533
Polymers17,2811
Non-polymers6722
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 48.240, 77.480
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 Myoglobin /


Mass: 17280.896 Da / Num. of mol.: 1 / Mutation: L29H, F43H, V68E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: swMB / Plasmid: pT7-7 / Cell line (production host): BL-21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHOR STATES THAT FE IN HEM SHOULD BE FE(II) ION

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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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: pH 7, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.7309 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7309 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. all: 14893 / Num. obs: 13961
Reflection shellResolution: 1.72→1.78 Å / % possible all: 98.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.72→8 Å / Num. parameters: 4351 / Num. restraintsaints: 5211 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rwork0.243 ---
all0.2458 14893 --
obs-13961 92.7 %-
Rfree--27.4 %RANDOM
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1400
Refinement stepCycle: LAST / Resolution: 1.72→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 44 126 1389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.962
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0238
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps0

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