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- PDB-2x2p: The flavoprotein NrdI from Bacillus cereus with the initially sem... -

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Basic information

Entry
Database: PDB / ID: 2x2p
TitleThe flavoprotein NrdI from Bacillus cereus with the initially semiquinone FMN cofactor in an intermediate radiation reduced state
ComponentsNRDI PROTEIN
KeywordsFLAVOPROTEIN / RIBONUCLEOTIDE REDUCTASE / FLAVODOXIN / ELECTRON TRANSFER
Function / homology
Function and homology information


protein modification process / FMN binding
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / FLAVIN MONONUCLEOTIDE / Protein NrdI
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsRohr, A.K. / Hersleth, H.P. / Andersson, K.K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Tracking Flavin Conformations in Protein Crystal Structures with Raman Spectroscopy and Qm/Mm Calculations
Authors: Rohr, A.K. / Hersleth, H.P. / Andersson, K.K.
History
DepositionJan 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: NRDI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3947
Polymers13,5391
Non-polymers8556
Water2,468137
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.955, 45.485, 56.200
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 NRDI PROTEIN / NRDI


Mass: 13539.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81G57
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.79 Å3/Da / Density % sol: 31.1 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 0.2 M ZINC ACETATE DIHYDRATE, 14 %(W/V) PEG 8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.7092
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7092 Å / Relative weight: 1
ReflectionResolution: 1.15→28.09 Å / Num. obs: 39780 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RLJ

1rlj


Resolution: 1.15→30 Å / Num. parameters: 10362 / Num. restraintsaints: 12808 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE FLAVIN COFACTOR IS IN AN INTERMEDIATE ONE ELECTRON STATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 -5 %RANDOM
all0.1526 37736 --
obs--94.7 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 920 / Occupancy sum non hydrogen: 1110.22
Refinement stepCycle: LAST / Resolution: 1.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 40 137 1111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0322
X-RAY DIFFRACTIONs_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.099

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