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- PDB-4e2g: Crystal structure of Cupin fold protein Sthe2323 from Sphaerobact... -

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Basic information

Entry
Database: PDB / ID: 4e2g
TitleCrystal structure of Cupin fold protein Sthe2323 from Sphaerobacter thermophilus
ComponentsCupin 2 conserved barrel domain protein
KeywordsStructural Genomics / Unknown Function / MCSG / PSI-biology / GEBA / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / NICKEL (II) ION / Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Cupin fold protein Sthe2323 from Sphaerobacter thermophilus
Authors: Chang, C. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Cupin 2 conserved barrel domain protein
B: Cupin 2 conserved barrel domain protein
C: Cupin 2 conserved barrel domain protein
D: Cupin 2 conserved barrel domain protein
E: Cupin 2 conserved barrel domain protein
F: Cupin 2 conserved barrel domain protein
G: Cupin 2 conserved barrel domain protein
H: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,07815
Polymers115,7068
Non-polymers3727
Water11,854658
1
A: Cupin 2 conserved barrel domain protein
B: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9853
Polymers28,9262
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-37 kcal/mol
Surface area11040 Å2
MethodPISA
2
C: Cupin 2 conserved barrel domain protein
D: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0244
Polymers28,9262
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-38 kcal/mol
Surface area11370 Å2
MethodPISA
3
E: Cupin 2 conserved barrel domain protein
F: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0444
Polymers28,9262
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-36 kcal/mol
Surface area11120 Å2
MethodPISA
4
G: Cupin 2 conserved barrel domain protein
H: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0244
Polymers28,9262
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-39 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.710, 52.623, 108.818
Angle α, β, γ (deg.)90.000, 91.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cupin 2 conserved barrel domain protein


Mass: 14463.205 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sthe_2323 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1C798
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris, 25% PEG3350, 20% glycerol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 92501 / Num. obs: 91471 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 25.38
Reflection shellResolution: 1.86→1.88 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.01 / Num. unique all: 2146 / % possible all: 93.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.63 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 4571 5 %RANDOM
Rwork0.1588 ---
all0.1614 91431 --
obs0.1614 91431 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.6 Å2 / Biso mean: 31.6264 Å2 / Biso min: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20.09 Å2
2---0.64 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 10 658 8001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027795
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.97310624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51823.033389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.637151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6421579
X-RAY DIFFRACTIONr_chiral_restr0.0720.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0226279
X-RAY DIFFRACTIONr_rigid_bond_restr1.69237795
X-RAY DIFFRACTIONr_sphericity_free30.7495261
X-RAY DIFFRACTIONr_sphericity_bonded17.357980
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 309 -
Rwork0.229 5760 -
all-6069 -
obs-6069 91.94 %
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)
10.02090.01190.03230.02510.02830.0571-0.00110.0023-0.0008-0.0022-0.00030.0004-0.01190.00350.00140.057-0.0002-0.00330.01910.00030.00416.824345.403498.0675
20.02760.039-0.01590.09050.02310.0755-0.00280.00040.001-0.01250.00090.0010.00330.00560.00190.05920.0017-0.00380.01830.00020.003513.406225.728100.243
30.0165-0.02950.01790.0767-0.00880.0426-0.00390.00110.00130.01110.00020.0006-0.00280.0040.00370.0578-0.0008-0.00130.0192-0.00080.003215.892353.872763.7213
40.02940.0088-0.02190.04030.00830.0238-0.0014-0.0006-0.00090.0036-0.0014-0.00060.00880.00170.00280.05760.0001-0.00120.01840.00020.00417.458334.975865.8395
50.01450.0071-0.01130.0191-0.03250.05540.0001-0.0003-0.00120.0005-0.001-0.00070.00230.00080.0010.05390.0002-0.00280.01860.00010.004569.143252.327470.1916
60.05020.02450.00680.02040.00480.0526-0.00390.00690.0029-0.00050.00210.00380.0001-0.00780.00180.05430.0003-0.00250.020.00070.002851.766243.058968.1078
70.0144-0.00270.01480.0391-0.01210.0176-0.00210.00170.00070.00450.0012-0.0022-0.002300.00080.05610-0.00230.0180.00040.004468.663928.065891.7089
80.0408-0.04810.03960.0767-0.03330.1156-0.0071-0.0105-0.00630.00590.00940.0039-0.0032-0.019-0.00230.05210.0007-0.00190.02130.00120.002751.287937.377293.0383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 123
2X-RAY DIFFRACTION2B10 - 123
3X-RAY DIFFRACTION3C1 - 123
4X-RAY DIFFRACTION4D8 - 123
5X-RAY DIFFRACTION5E9 - 112
6X-RAY DIFFRACTION6F9 - 123
7X-RAY DIFFRACTION7G9 - 123
8X-RAY DIFFRACTION8H9 - 123

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