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- PDB-4oo3: Crystal structure of a putative oxidoreductase (PARMER_00841) fro... -

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Basic information

Entry
Database: PDB / ID: 4oo3
TitleCrystal structure of a putative oxidoreductase (PARMER_00841) from Parabacteroides merdae ATCC 43184 at 2.23 A resolution
Componentshypothetical protein
KeywordsOXIDOREDUCTASE / NAD-binding Rossmann fold (PF01408) / putative oxidoreductase C terminal domain (PF16490) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyPutative oxidoreductase, C-terminal / Putative oxidoreductase C terminal domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Oxidoreduct_C domain-containing protein
Function and homology information
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.23 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PARMER_00841) from Parabacteroides merdae ATCC 43184 at 2.23 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)50,2211
Polymers50,2211
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.437, 93.510, 95.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 50221.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_00841, ZP_02030865.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7ABT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-466 OF THE TARGET SEQUENCE.

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium acetate, 30.0% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97895,0.97959
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978951
30.979591
ReflectionResolution: 2.23→27.528 Å / Num. obs: 21588 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.759 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.23-2.310.5581.66838391295.3
2.31-2.40.4391.96486381395.1
2.4-2.510.3782.57370402197.2
2.51-2.640.2673.27184394797.5
2.64-2.810.2074.27449407396.9
2.81-3.020.1445.76658383895.7
3.02-3.330.0819.47266401095.8
3.33-3.810.05115.47437399897.4
3.81-4.780.03121.76767388995.2
4.780.02426.57400401196

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.23→27.528 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.401 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.215
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1103 5.1 %RANDOM
Rwork0.1863 ---
obs0.1883 21538 98.35 %-
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 max: 117.14 Å2 / Biso mean: 41.8434 Å2 / Biso min: 17.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å20 Å2
2--2.89 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.23→27.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 0 162 3627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193564
X-RAY DIFFRACTIONr_bond_other_d0.0010.023371
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9644841
X-RAY DIFFRACTIONr_angle_other_deg0.69337790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82925.521163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31315585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.804159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02779
X-RAY DIFFRACTIONr_mcbond_it1.9264.8611759
X-RAY DIFFRACTIONr_mcbond_other1.9254.8561758
X-RAY DIFFRACTIONr_mcangle_it3.0559.0982198
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 77 -
Rwork0.284 1471 -
all-1548 -
obs--98.41 %
Refinement TLS params.Method: refined / Origin x: 45.503 Å / Origin y: 11.162 Å / Origin z: 23.727 Å
111213212223313233
T0.0972 Å2-0.0004 Å20.0081 Å2-0.044 Å2-0.0204 Å2--0.1435 Å2
L0.6908 °2-0.0918 °20.3043 °2-0.964 °20.0816 °2--2.1191 °2
S-0.0127 Å °-0.1122 Å °0.0718 Å °-0.1464 Å °-0.0007 Å °0.0112 Å °0.2236 Å °0.1019 Å °0.0134 Å °

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