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- PDB-4ici: Crystal structure of a putative flavoprotein (BACEGG_01620) from ... -

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Basic information

Entry
Database: PDB / ID: 4ici
TitleCrystal structure of a putative flavoprotein (BACEGG_01620) from Bacteroides eggerthii DSM 20697 at 1.40 A resolution
ComponentsPutative flavoprotein
KeywordsFLAVOPROTEIN / PF12682 family protein / flavodoxin_4 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyFlavodoxin domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FLAVIN MONONUCLEOTIDE / Unknown ligand / :
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative flavoprotein (BACEGG_01620) from Bacteroides eggerthii DSM 20697 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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: Putative flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8757
Polymers18,9941
Non-polymers8816
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.625, 85.625, 58.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative flavoprotein


Mass: 18994.205 Da / Num. of mol.: 1 / Fragment: UNP residues 21-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_01620, ZP_03458840.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AGU1

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Non-polymers , 5 types, 261 molecules

#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-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-190 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.40M tri-Sodium Citrate, 0.1M sodium HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401,0.979493,0.979199
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9794931
30.9791991
ReflectionResolution: 1.4→29.067 Å / Num. all: 40475 / Num. obs: 40475 / % possible obs: 98.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.318 Å2 / Rsym value: 0.085 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.443.90.6892.21147829760.68999.5
1.44-1.483.90.5692.71139729530.56999.5
1.48-1.523.90.4513.31121228880.45199.3
1.52-1.573.90.36441073327550.36499
1.57-1.623.90.2974.71046226670.29798.8
1.62-1.673.90.2465.51016325950.24698.6
1.67-1.743.90.2186.1973424860.21898.6
1.74-1.813.90.1657.3953324220.16598.3
1.81-1.893.90.1278.6896822740.12798.3
1.89-1.983.90.09810.5867322080.09898.2
1.98-2.093.90.08212.1815220780.08298.3
2.09-2.213.90.07213.9777719830.07298.4
2.21-2.373.90.06715.1724018530.06798.1
2.37-2.563.90.06315.5669117340.06398.1
2.56-2.83.80.06216.4613515970.06298
2.8-3.133.70.06518521914230.06597.7
3.13-3.613.80.06620.5474712600.06696.5
3.61-4.434.20.04922.7448110670.04996.8
4.43-6.264.20.04621.834698220.04695.7
6.26-29.0674.20.04621.918434340.04692.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMACrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.067 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.362 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.043
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. HEPES (EPE) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 4. A FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS MODELED IN THE ACTIVE SITE BASED ON THE ELECTRON DENSITY. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED ADJACENT TO THE ISOALLOXAZINE RING OF FMN.
RfactorNum. reflection% reflectionSelection details
Rfree0.1468 2029 5 %RANDOM
Rwork0.1147 ---
obs0.1163 40456 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 58.86 Å2 / Biso mean: 17.776 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 64 255 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221363
X-RAY DIFFRACTIONr_bond_other_d0.0010.02938
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0131864
X-RAY DIFFRACTIONr_angle_other_deg1.02732310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4924.16748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65515221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.613156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
X-RAY DIFFRACTIONr_mcbond_it2.4193816
X-RAY DIFFRACTIONr_mcbond_other1.6033328
X-RAY DIFFRACTIONr_mcangle_it3.44151326
X-RAY DIFFRACTIONr_scbond_it4.6058547
X-RAY DIFFRACTIONr_scangle_it6.03311530
X-RAY DIFFRACTIONr_rigid_bond_restr1.90632301
X-RAY DIFFRACTIONr_sphericity_free7.6583267
X-RAY DIFFRACTIONr_sphericity_bonded4.2332265
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 143 -
Rwork0.194 2821 -
all-2964 -
obs--99.16 %

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