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- PDB-3mc3: Crystal structure of DsrE/DsrF-like family protein (NP_342589.1) ... -

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Basic information

Entry
Database: PDB / ID: 3mc3
TitleCrystal structure of DsrE/DsrF-like family protein (NP_342589.1) from SULFOLOBUS SOLFATARICUS at 1.49 A resolution
ComponentsDsrE/DsrF-like family protein
Keywordsstructural genomics / unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.49 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DsrE/DsrF-like family protein (NP_342589.1) from SULFOLOBUS SOLFATARICUS at 1.49 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DsrE/DsrF-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0552
Polymers16,0191
Non-polymers351
Water2,000111
1
A: DsrE/DsrF-like family protein
hetero molecules

A: DsrE/DsrF-like family protein
hetero molecules

A: DsrE/DsrF-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1646
Polymers48,0583
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5660 Å2
ΔGint-112 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.070, 64.070, 105.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

21A-227-

HOH

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Components

#1: Protein DsrE/DsrF-like family protein


Mass: 16019.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO1125 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97Z18
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...1. 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 THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5.0000% polyethylene glycol 3000, 40.0000% polyethylene glycol 400, 0.1M MES pH 6.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97871,0.97831
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978711
30.978311
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.772
11K, H, -L20.228
ReflectionResolution: 1.49→26.832 Å / Num. obs: 26406 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.255 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.49-1.540.315269194712194.9
1.54-1.60.2422.773174986195.3
1.6-1.680.1773.680715506195.6
1.68-1.770.1215.275825156196.1
1.77-1.880.087.673725020196.1
1.88-2.020.05411.271744886196.3
2.02-2.230.03616.977715301196.7
2.23-2.550.02822.273575029196.1
2.55-3.210.0222873995059196.7
3.21-26.8320.01734.975135154197.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.49→26.832 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.693 / SU ML: 0.027 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.009 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. THE DATA IS TWINNED. THE FINAL TWIN FRACTION WAS REFINED TO 0.228 USING THE OPERATOR "K,H,-L". 5.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION. THE LYSINE RESIDUES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY). 6. CYSTEINE 93 IS OXIDIZED AND IS MODELED AS S-OXY CYSTEINE (CSX). 7. CHLORIDE ION (CL) IS MODELED FROM THE PROTEIN BUFFER SOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 1355 5.1 %RANDOM
Rwork0.122 ---
obs0.123 26404 99.81 %-
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: 56.28 Å2 / Biso mean: 14.739 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.49→26.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 1 111 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221076
X-RAY DIFFRACTIONr_bond_other_d0.0030.02743
X-RAY DIFFRACTIONr_angle_refined_deg1.5092.0041467
X-RAY DIFFRACTIONr_angle_other_deg0.93431840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61725.10647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32615.158221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.774154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02208
X-RAY DIFFRACTIONr_mcbond_it0.8161.5640
X-RAY DIFFRACTIONr_mcbond_other0.2241.5258
X-RAY DIFFRACTIONr_mcangle_it1.42221050
X-RAY DIFFRACTIONr_scbond_it2.7093436
X-RAY DIFFRACTIONr_scangle_it4.1644.5404
LS refinement shellResolution: 1.49→1.528 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.165 1927 -
obs--98.72 %
Refinement TLS params.Method: refined / Origin x: 10.354 Å / Origin y: 10.474 Å / Origin z: 59.661 Å
111213212223313233
T0.0657 Å2-0.0198 Å2-0.0095 Å2-0.0642 Å20 Å2--0.0292 Å2
L1.0385 °20.1395 °20.7044 °2-0.7372 °20.2764 °2--1.4646 °2
S-0.0531 Å °-0.0255 Å °0.1132 Å °0.0077 Å °0.0101 Å °-0.0839 Å °-0.0852 Å °0.0836 Å °0.0429 Å °

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