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- PDB-3f7c: Crystal structure of a duf416 family protein (maqu_0942) from mar... -

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Basic information

Entry
Database: PDB / ID: 3f7c
TitleCrystal structure of a duf416 family protein (maqu_0942) from marinobacter aquaeolei vt8 at 2.00 A resolution
Componentsprotein of unknown function (DUF416)
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyYP_001051499.1 fold like / YP_001051499.1 domain like / Protein of unknown function DUF416 / YP001051499.1-like domain superfamily / Protein of unknown function (DUF416) / Up-down Bundle / Mainly Alpha / CITRIC ACID / DUF416 family protein
Function and homology information
Biological speciesMarinobacter aquaeolei VT8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (DUF416) (YP_958225.1) from MARINOBACTER AQUAEOLEI VT8 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: protein of unknown function (DUF416)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9943
Polymers22,7791
Non-polymers2152
Water2,180121
1
A: protein of unknown function (DUF416)
hetero molecules

A: protein of unknown function (DUF416)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9886
Polymers45,5582
Non-polymers4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area6330 Å2
ΔGint-56 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.998, 76.998, 91.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein protein of unknown function (DUF416)


Mass: 22778.768 Da / Num. of mol.: 1 / Mutation: K168Y, K169Y, Q170Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei VT8 (bacteria) / Gene: Maqu_0942, YP_958225.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1TZ69
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT WAS ENGINEERED WITH THREE MUTATIONS K168Y, K169Y AND Q170Y. THE SITES OF MUTATIONS WERE SELECTED FROM HIGH ENTROPY SITES PREDICTED BY THE UCLA SURFACE ENTROPY REDUCTION SERVER.

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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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.0M sodium citrate, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 2→29.424 Å / Num. obs: 20811 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 37.979 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 4.107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.055.70.8350.9865815100.83599.8
2.05-2.115.60.6970.6848915110.697100
2.11-2.175.70.4841.5836414570.484100
2.17-2.245.80.3821.9812414100.382100
2.24-2.315.70.3820.8765113540.382100
2.31-2.395.80.242.9769513340.24100
2.39-2.485.70.1833.9739012870.183100
2.48-2.585.80.1584.4706712250.158100
2.58-2.75.70.1414.2675611770.141100
2.7-2.835.80.1116.1657611410.111100
2.83-2.9880.1146861910760.114100
2.98-3.1690.1125.6902410060.112100
3.16-3.3810.60.0926.5102039630.092100
3.38-3.6511.30.0846.4101018960.084100
3.65-411.30.0758.192098130.075100
4-4.4711.40.0728.385177470.072100
4.47-5.1611.30.0698.575436680.069100
5.16-6.3211.30.0758.362675540.075100
6.32-8.94110.0735.748304390.073100
8.94-29.4310.20.0855.324712430.08597.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.424 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.148 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.118
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. CITRATE AND SODIUM MODELED ARE PRESENT IN CRYSTALLIZATION CONDITION. 5. THERE ARE SOME UNMODELED NON-PROTEIN DENSITIES NEAR RESIDUE A19.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1067 5.1 %RANDOM
Rwork0.172 ---
obs0.173 20774 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.91 Å2 / Biso mean: 35.327 Å2 / Biso min: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→29.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 14 121 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221624
X-RAY DIFFRACTIONr_bond_other_d0.0020.021090
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9782203
X-RAY DIFFRACTIONr_angle_other_deg0.92632656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9045204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65524.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88115277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.811511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_mcbond_it1.8843999
X-RAY DIFFRACTIONr_mcbond_other0.5533404
X-RAY DIFFRACTIONr_mcangle_it3.14251591
X-RAY DIFFRACTIONr_scbond_it5.518625
X-RAY DIFFRACTIONr_scangle_it7.90311609
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 79 -
Rwork0.274 1431 -
all-1510 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -4.9493 Å / Origin y: 33.5066 Å / Origin z: 25.0593 Å
111213212223313233
T0.0315 Å20.0158 Å20.0114 Å2-0.0534 Å2-0.006 Å2--0.0493 Å2
L1.0894 °20.2092 °20.4322 °2-0.261 °20.0495 °2--0.717 °2
S-0.0385 Å °-0.0618 Å °-0.0086 Å °-0.0495 Å °0.0329 Å °-0.0439 Å °0.0856 Å °0.1136 Å °0.0057 Å °

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