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- PDB-3ebr: Crystal structure of an rmlc-like cupin protein (reut_a0381) from... -

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Basic information

Entry
Database: PDB / ID: 3ebr
TitleCrystal structure of an rmlc-like cupin protein (reut_a0381) from ralstonia eutropha jmp134 at 2.60 A resolution
Componentsuncharacterized RmlC-like cupin
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


ChrR-like cupin domain / ChrR Cupin-like domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cupin_7 domain-containing protein
Similarity search - Component
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of RmlC-like cupin with unknown function (YP_294607.1) from RALSTONIA EUTROPHA JMP134 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.classification / _software.name
Revision 1.3Jul 24, 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized RmlC-like cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6855
Polymers18,2611
Non-polymers4244
Water45025
1
A: uncharacterized RmlC-like cupin
hetero molecules

A: uncharacterized RmlC-like cupin
hetero molecules

A: uncharacterized RmlC-like cupin
hetero molecules

A: uncharacterized RmlC-like cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74020
Polymers73,0434
Non-polymers1,69816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
Buried area16580 Å2
ΔGint-42 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.157, 91.157, 48.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-162-

PEG

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Components

#1: Protein uncharacterized RmlC-like cupin


Mass: 18260.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Gene: YP_294607.1, Reut_A0381 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q476C0
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 60.0% polyethylene glycol 200, 0.1M HEPES pH 6.5, 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: 0.91837,0.97941,0.97854
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 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
20.979411
30.978541
ReflectionResolution: 2.6→28.831 Å / Num. obs: 6713 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 76.248 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.674.80.5962.222904760.596100
2.67-2.744.90.4363.122834700.436100
2.74-2.824.80.3753.421584510.375100
2.82-2.914.80.2894.521764520.289100
2.91-34.80.2036.220504300.203100
3-3.114.80.1717.720264190.171100
3.11-3.224.70.11810.619644140.118100
3.22-3.364.80.0991318443840.099100
3.36-3.514.70.07915.717993830.079100
3.51-3.684.80.07419.617333640.074100
3.68-3.884.70.07321.715753370.073100
3.88-4.114.60.06725.415713390.067100
4.11-4.394.60.05829.514383100.058100
4.39-4.754.60.0552913562940.055100
4.75-5.24.50.04630.312262700.046100
5.2-5.814.50.05628.411222520.056100
5.81-6.714.40.06926.39892230.06999.9
6.71-8.224.20.06226.58311970.06299.8
8.22-11.634.10.05827.16431570.05899.9
11.63-28.833.50.05428.1318910.05492.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.6→28.831 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.026 / SU ML: 0.245 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.318
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PEG MOLECULES FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 498 7.4 %RANDOM
Rwork0.227 ---
obs0.229 6707 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.51 Å2 / Biso mean: 48.516 Å2 / Biso min: 29.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 28 25 1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221298
X-RAY DIFFRACTIONr_bond_other_d0.0040.02848
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9331764
X-RAY DIFFRACTIONr_angle_other_deg1.53232063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4045158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.45623.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17315185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.639155
X-RAY DIFFRACTIONr_chiral_restr0.070.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021439
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02266
X-RAY DIFFRACTIONr_nbd_refined0.1320.3186
X-RAY DIFFRACTIONr_nbd_other0.120.3790
X-RAY DIFFRACTIONr_nbtor_refined0.1620.5595
X-RAY DIFFRACTIONr_nbtor_other0.0770.5633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.565
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0850.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.58
X-RAY DIFFRACTIONr_mcbond_it1.0773816
X-RAY DIFFRACTIONr_mcbond_other0.1733316
X-RAY DIFFRACTIONr_mcangle_it1.86951277
X-RAY DIFFRACTIONr_scbond_it3.0988570
X-RAY DIFFRACTIONr_scangle_it4.34311487
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 37 -
Rwork0.34 439 -
all-476 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 34.5814 Å / Origin y: 13.8228 Å / Origin z: 20.91 Å
111213212223313233
T-0.041 Å20.1226 Å20.1029 Å2-0.0195 Å2-0.0137 Å2--0.1081 Å2
L2.4513 °2-0.0432 °20.1002 °2-3.3662 °20.3986 °2--4.187 °2
S0.4224 Å °0.2154 Å °0.394 Å °-0.2277 Å °-0.3867 Å °0.4321 Å °-0.2683 Å °-0.4346 Å °-0.0356 Å °

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