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Entry
Database: PDB / ID: 3cjx
TitleCrystal structure of a protein of unknown function with a cupin-like fold (reut_b4571) from ralstonia eutropha jmp134 at 2.60 A resolution
ComponentsProtein of unknown function with a cupin-like fold
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyRmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein with a cupin-like fold and unknown function (YP_298765.1) from Ralstonia eutropha JMP134 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein of unknown function with a cupin-like fold
B: Protein of unknown function with a cupin-like fold
C: Protein of unknown function with a cupin-like fold
D: Protein of unknown function with a cupin-like fold
E: Protein of unknown function with a cupin-like fold
F: Protein of unknown function with a cupin-like fold
G: Protein of unknown function with a cupin-like fold
H: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,53531
Polymers147,6088
Non-polymers1,92723
Water3,297183
1
A: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7314
Polymers18,4511
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7314
Polymers18,4511
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5472
Polymers18,4511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7675
Polymers18,4511
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6754
Polymers18,4511
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5472
Polymers18,4511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8596
Polymers18,4511
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6794
Polymers18,4511
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Protein of unknown function with a cupin-like fold
B: Protein of unknown function with a cupin-like fold
C: Protein of unknown function with a cupin-like fold
D: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,77615
Polymers73,8044
Non-polymers97211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-85.7 kcal/mol
Surface area25420 Å2
MethodPISA
10
E: Protein of unknown function with a cupin-like fold
F: Protein of unknown function with a cupin-like fold
G: Protein of unknown function with a cupin-like fold
H: Protein of unknown function with a cupin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,75916
Polymers73,8044
Non-polymers95512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-88.6 kcal/mol
Surface area25100 Å2
MethodPISA
11


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24000 Å2
ΔGint-185.4 kcal/mol
Surface area47940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.210, 89.130, 212.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End label comp-ID: ALA / Refine code: 4

Dom-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ILEAA7 - 1684 - 165
2GLUBB11 - 1688 - 165
3GLUCC11 - 1688 - 165
4GLNDD10 - 1687 - 165
5THREE8 - 1685 - 165
6LYSFF12 - 1689 - 165
7LYSGG12 - 1689 - 165
8GLUHH11 - 1688 - 165
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY INDICATES THAT THE MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Protein of unknown function with a cupin-like fold


Mass: 18450.947 Da / Num. of mol.: 8 / Fragment: Residues 5-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_298765.1, Reut_B4571 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46SG3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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. THE CONSTRUCT CONTAINS RESIDUES 5-168 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 1.6M (NH4)2SO4, 0.1M Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9798, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007 / 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
10.95371
20.97981
30.97961
ReflectionResolution: 2.6→29.604 Å / Num. obs: 46886 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.514 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.690.3462.3134108230195.1
2.69-2.80.2732.9152169097199
2.8-2.930.2014150019007198.8
2.93-3.080.1435.6146478679199
3.08-3.270.17.9147198713198.7
3.27-3.520.06611.4148988821198.9
3.52-3.880.0514.7154509074198.7
3.88-4.430.03718.8148778778198.6
4.43-5.570.02922.9150168822198.3
5.57-29.6040.02524.9151128682194.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.604 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 21.138 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.825 / ESU R Free: 0.298
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 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 ...Details: 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. ELECTRON DENSITIES BETWEEN RESIDUES 137 AND 132 IN THE B SUBUNIT WERE DISORDERED AND THESE RESIDUES WERE NOT MODELED. 5. SULFATE AND CHLORIDE IONS FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL FROM THE CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2366 5.1 %RANDOM
Rwork0.203 ---
obs0.205 46841 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.895 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2---1.22 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9688 0 109 183 9980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210145
X-RAY DIFFRACTIONr_bond_other_d0.0020.026448
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.94613857
X-RAY DIFFRACTIONr_angle_other_deg1.012315731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.57251271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66524.156450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.351525
X-RAY DIFFRACTIONr_chiral_restr0.0850.21485
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211498
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022118
X-RAY DIFFRACTIONr_nbd_refined0.2030.32002
X-RAY DIFFRACTIONr_nbd_other0.1750.36484
X-RAY DIFFRACTIONr_nbtor_refined0.1910.54850
X-RAY DIFFRACTIONr_nbtor_other0.0890.55169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5609
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1110.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1420.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3310.57
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1320.51
X-RAY DIFFRACTIONr_mcbond_it1.09436414
X-RAY DIFFRACTIONr_mcbond_other0.28732590
X-RAY DIFFRACTIONr_mcangle_it1.764510087
X-RAY DIFFRACTIONr_scbond_it3.14284292
X-RAY DIFFRACTIONr_scangle_it4.431113764
Refine LS restraints NCS

Ens-ID: 1 / Number: 1743 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.370.5
2BMEDIUM POSITIONAL0.320.5
3CMEDIUM POSITIONAL0.380.5
4DMEDIUM POSITIONAL0.290.5
5EMEDIUM POSITIONAL0.430.5
6FMEDIUM POSITIONAL0.320.5
7GMEDIUM POSITIONAL0.370.5
8HMEDIUM POSITIONAL0.310.5
1AMEDIUM THERMAL0.272
2BMEDIUM THERMAL0.252
3CMEDIUM THERMAL0.272
4DMEDIUM THERMAL0.22
5EMEDIUM THERMAL0.32
6FMEDIUM THERMAL0.232
7GMEDIUM THERMAL0.242
8HMEDIUM THERMAL0.232
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 181 -
Rwork0.279 3107 -
all-3288 -
obs--95.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99280.4098-0.68781.6199-0.72710.61190.015-0.09010.2207-0.11470.06190.2018-0.1174-0.0762-0.0769-0.0756-0.077-0.0393-0.0394-0.0286-0.08327.4982-39.993680.0175
22.91820.4305-1.79351.29110.23112.40320.0263-0.358-0.05640.2844-0.0221-0.33130.08730.2115-0.0042-0.0327-0.0665-0.0662-0.12880.0066-0.114719.9785-53.221793.053
31.17941.31280.22611.71790.75461.0292-0.08830.0550.1109-0.10950.0250.20320.0387-0.18830.0633-0.0996-0.08860.0132-0.08360.0107-0.095230.6506-22.068575.5995
42.7640.3065-0.92722.18550.32780.8380.0044-0.4241-0.24210.5208-0.13-0.03280.2810.04240.12560.1103-0.1129-0.03920.0389-0.0179-0.072136.0984-27.228197.6674
51.74840.3938-0.09771.50430.87531.4504-0.02440.1884-0.119-0.30180.0065-0.0276-0.09180.06740.018-0.0666-0.08370.0267-0.0536-0.0301-0.093276.329811.978559.0495
61.99550.4039-0.8711.66650.91811.7345-0.0537-0.2872-0.32650.37310.0801-0.28740.31280.2647-0.0264-0.011-0.079-0.0463-0.05170.006-0.047681.940311.066981.4979
71.51390.0845-0.30461.38420.94110.72680.0768-0.1312-0.10370.0844-0.0094-0.30830.03630.2313-0.0673-0.0606-0.0411-0.0052-0.10060.016-0.073759.276-8.098583.6921
81.47231.6424-0.66313.5335-0.70470.3587-0.15060.29710.2206-0.4540.26390.098-0.0438-0.0674-0.1133-0.0748-0.0437-0.0448-0.02070.0152-0.110348.35164.341266.631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1684 - 165
2X-RAY DIFFRACTION2BB11 - 1688 - 165
3X-RAY DIFFRACTION3CC11 - 1688 - 165
4X-RAY DIFFRACTION4DD10 - 1687 - 165
5X-RAY DIFFRACTION5EE8 - 1685 - 165
6X-RAY DIFFRACTION6FF12 - 1689 - 165
7X-RAY DIFFRACTION7GG12 - 1689 - 165
8X-RAY DIFFRACTION8HH11 - 1688 - 165

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