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- PDB-4a3u: X-structure of the old yellow enzyme homologue from zymomonas mob... -

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Basic information

Entry
Database: PDB / ID: 4a3u
TitleX-structure of the old yellow enzyme homologue from zymomonas mobilis (NCR)
ComponentsNADH\:FLAVIN OXIDOREDUCTASE/NADH OXIDASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / : / NICOTINAMIDE / NADH:flavin oxidoreductase/NADH oxidase
Similarity search - Component
Biological speciesZYMOMONAS MOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHoeffken, H.W.
CitationJournal: Chembiochem / Year: 2012
Title: Crystal Structure Determination and Mutagenesis Analysis of the Ene Reductase Ncr.
Authors: Reich, S. / Hoeffken, H.W. / Rosche, B. / Nestl, B.M. / Hauer, B.
History
DepositionOct 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
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_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.ptnr1_symmetry / _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.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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH\:FLAVIN OXIDOREDUCTASE/NADH OXIDASE
B: NADH\:FLAVIN OXIDOREDUCTASE/NADH OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,49313
Polymers79,0712
Non-polymers1,42211
Water9,224512
1
A: NADH\:FLAVIN OXIDOREDUCTASE/NADH OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2356
Polymers39,5361
Non-polymers7005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADH\:FLAVIN OXIDOREDUCTASE/NADH OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2587
Polymers39,5361
Non-polymers7236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 90.500, 76.600
Angle α, β, γ (deg.)90.00, 108.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NADH\:FLAVIN OXIDOREDUCTASE/NADH OXIDASE / NCR


Mass: 39535.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZYMOMONAS MOBILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5NLA1

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Non-polymers , 6 types, 523 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.19 Å3/Da / Density % sol: 43.73 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: THE CRYSTALS OF NCR WERE GROWN BY THE SITTING DROP METHOD IN A BUFFER CONTAINING 15% PEG 8000, 0.1 M NA CACODYLATE, AND 0.2 M CA ACETATE, AT PH 6.5. 0.4 MICRO L DIOXAN (30%) AND 0.4 MICRO L ...Details: THE CRYSTALS OF NCR WERE GROWN BY THE SITTING DROP METHOD IN A BUFFER CONTAINING 15% PEG 8000, 0.1 M NA CACODYLATE, AND 0.2 M CA ACETATE, AT PH 6.5. 0.4 MICRO L DIOXAN (30%) AND 0.4 MICRO L ISOPROPANOL WERE ADDED TO THE MICRO L CRYSTALLIZATION DROPS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.1 Å / Num. obs: 64934 / % possible obs: 86.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.59
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3 / % possible all: 49.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GQA

2gqa


Resolution: 1.7→43.06 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.77 / SU B: 3.603 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30275 3242 5 %RANDOM
Rwork0.23892 ---
obs0.24205 61700 86.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.07 Å2
2--0.08 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 93 512 6142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025780
X-RAY DIFFRACTIONr_bond_other_d0.0010.023953
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9747867
X-RAY DIFFRACTIONr_angle_other_deg1.10539575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74123.282262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66715901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9971546
X-RAY DIFFRACTIONr_chiral_restr0.1070.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021219
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 129 -
Rwork0.249 2205 -
obs--42.67 %

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