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- PDB-3d82: Crystal structure of a cupin-2 domain containing protein (sfri_35... -

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Basic information

Entry
Database: PDB / ID: 3d82
TitleCrystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella frigidimarina ncimb 400 at 2.05 A resolution
ComponentsCupin 2, conserved barrel domain protein
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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
NICKEL (II) ION / Unknown ligand / Cupin 2, conserved barrel domain protein
Similarity search - Component
Biological speciesShewanella frigidimarina NCIMB 400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Domain of Unknown Function with a Cupin Fold (YP_752209.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,88917
Polymers61,4115
Non-polymers47812
Water4,270237
1
D: Cupin 2, conserved barrel domain protein
E: Cupin 2, conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8668
Polymers24,5642
Non-polymers3026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-54 kcal/mol
Surface area9610 Å2
MethodPISA
2
A: Cupin 2, conserved barrel domain protein
hetero molecules

A: Cupin 2, conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6826
Polymers24,5642
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3810 Å2
ΔGint-52 kcal/mol
Surface area9940 Å2
MethodPISA
3
B: Cupin 2, conserved barrel domain protein
C: Cupin 2, conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6826
Polymers24,5642
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-48 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.920, 95.140, 237.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-554-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61A
71B
81C
91D
101E
111A
121B
131C
141D
151E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPHEPHE4AA5 - 646 - 65
21VALVALPHEPHE4BB5 - 646 - 65
31VALVALPHEPHE4CC5 - 646 - 65
41VALVALPHEPHE4DD5 - 646 - 65
51VALVALPHEPHE4EE5 - 646 - 65
62ARGARGASPASP4AA65 - 6666 - 67
72ARGARGASPASP4BB65 - 6666 - 67
82ARGARGASPASP4CC65 - 6666 - 67
92ARGARGASPASP4DD65 - 6666 - 67
102ARGARGASPASP4EE65 - 6666 - 67
113GLNGLNARGARG6AA67 - 10168 - 102
123GLNGLNARGARG6BB67 - 10168 - 102
133GLNGLNARGARG6CC67 - 10168 - 102
143GLNGLNARGARG6DD67 - 10168 - 102
153GLNGLNARGARG6EE67 - 10168 - 102
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Cupin 2, conserved barrel domain protein


Mass: 12282.178 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina NCIMB 400 (bacteria)
Gene: YP_752209.1, Sfri_3543 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q07X94
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT INCLUDES AMINO ACIDS 1 TO 101 OF THE FULL-LENGTH PROTEIN OF 121 AMINO ACIDS AND WAS ...THE CONSTRUCT INCLUDES AMINO ACIDS 1 TO 101 OF THE FULL-LENGTH PROTEIN OF 121 AMINO ACIDS AND 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2000M K2NO3, 20.0000% PEG-3350, No Buffer pH 6., NANODROP, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97929,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
30.979181
ReflectionResolution: 2.05→27.853 Å / Num. obs: 40296 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.405 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.120.351.910533625883.7
2.12-2.210.2752.816237821798.5
2.21-2.310.2133.815643767799.5
2.31-2.430.1594.815444760799.4
2.43-2.580.1096.815599767799.5
2.58-2.780.089.316045784899.4
2.78-3.060.05413.415859775999.1
3.06-3.50.03619.115775768398.5
3.5-4.40.02625.915616753296.7
4.40.02328.615934753194.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→27.853 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.207 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.153
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF NI ION. 5. AN UNKNOWN LIGAND (UNL) IS MODELED NEXT TO THE NI ION IN EACH CHAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2018 5 %RANDOM
Rwork0.186 ---
obs0.187 40280 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---1.93 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.05→27.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 62 237 4469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224397
X-RAY DIFFRACTIONr_bond_other_d0.0030.022986
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9425940
X-RAY DIFFRACTIONr_angle_other_deg1.2337292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1045520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08525.216232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80515794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1081518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024877
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02895
X-RAY DIFFRACTIONr_nbd_refined0.1680.2591
X-RAY DIFFRACTIONr_nbd_other0.1420.22830
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22003
X-RAY DIFFRACTIONr_nbtor_other0.0720.22249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.214
X-RAY DIFFRACTIONr_mcbond_it1.13222702
X-RAY DIFFRACTIONr_mcbond_other0.23221024
X-RAY DIFFRACTIONr_mcangle_it1.83344189
X-RAY DIFFRACTIONr_scbond_it3.50661981
X-RAY DIFFRACTIONr_scangle_it4.7781741
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A809MEDIUM POSITIONAL0.360.5
2B809MEDIUM POSITIONAL0.290.5
3C809MEDIUM POSITIONAL0.230.5
4D809MEDIUM POSITIONAL0.210.5
5E809MEDIUM POSITIONAL0.280.5
1A449LOOSE POSITIONAL0.425
2B449LOOSE POSITIONAL0.485
3C449LOOSE POSITIONAL0.455
4D449LOOSE POSITIONAL0.285
5E449LOOSE POSITIONAL0.325
1A809MEDIUM THERMAL0.652
2B809MEDIUM THERMAL0.62
3C809MEDIUM THERMAL0.642
4D809MEDIUM THERMAL0.62
5E809MEDIUM THERMAL0.682
1A449LOOSE THERMAL2.510
2B449LOOSE THERMAL1.7310
3C449LOOSE THERMAL1.5410
4D449LOOSE THERMAL1.5510
5E449LOOSE THERMAL1.610
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 150 -
Rwork0.262 2552 -
all-2702 -
obs--91.41 %
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)
11.07270.1174-0.55166.99551.51781.7841-0.42490.1556-0.1219-0.29180.18371.4460.08940.29260.2412-0.1844-0.0182-0.0272-0.02470.23780.2831-17.047839-5.3581
22.1481-0.3083-0.27044.9927-1.53382.4459-0.0361-0.1004-0.2439-0.20510.25750.86230.1581-0.432-0.2214-0.1225-0.025-0.1226-0.03330.05-0.027-4.244729.7104-18.9824
32.33720.0512-0.6342.5749-0.53743.1383-0.05450.1325-0.0677-0.3186-0.0387-0.06680.13370.03580.0932-0.06830.0187-0.1008-0.1704-0.0056-0.203913.22235.2467-29.4753
42.2366-1.01281.06873.6381-0.61332.5084-0.0869-0.00040.17430.3712-0.0846-0.45680.07420.17390.1715-0.1218-0.0067-0.0882-0.11750.0168-0.174218.209151.0282-42.5254
52.0286-1.21170.42573.1252-0.6481.8408-0.07160.12770.3358-0.0178-0.1177-0.1938-0.11970.06130.1894-0.1465-0.0272-0.0643-0.11120.003-0.16718.365365.3943-52.9275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1011 - 102
2X-RAY DIFFRACTION2BB1 - 1012 - 102
3X-RAY DIFFRACTION3CC1 - 1012 - 102
4X-RAY DIFFRACTION4DD0 - 1011 - 102
5X-RAY DIFFRACTION5EE0 - 1011 - 102

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