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- PDB-2xla: Structure and metal-loading of a soluble periplasm cupro-protein:... -

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Basic information

Entry
Database: PDB / ID: 2xla
TitleStructure and metal-loading of a soluble periplasm cupro-protein: Cu- CucA-closed
ComponentsSLL1785 PROTEIN
KeywordsMETAL BINDING PROTEIN / CUPIN
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / UREA / Sll1785 protein
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWaldron, K.J. / Firbank, S.J. / Dainty, S.J. / Perez-Rama, M. / Tottey, S. / Robinson, N.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure and Metal Loading of a Soluble Periplasm Cuproprotein.
Authors: Waldron, K.J. / Firbank, S.J. / Dainty, S.J. / Perez-Rama, M. / Tottey, S. / Robinson, N.J.
History
DepositionJul 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SLL1785 PROTEIN
B: SLL1785 PROTEIN
C: SLL1785 PROTEIN
D: SLL1785 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,02812
Polymers107,5334
Non-polymers4948
Water19,2581069
1
A: SLL1785 PROTEIN
B: SLL1785 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0146
Polymers53,7672
Non-polymers2474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-29.9 kcal/mol
Surface area18790 Å2
MethodPISA
2
C: SLL1785 PROTEIN
D: SLL1785 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0146
Polymers53,7672
Non-polymers2474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-29.5 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.310, 72.510, 262.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SLL1785 PROTEIN / CUCA


Mass: 26883.352 Da / Num. of mol.: 4 / Fragment: RESIDUES 31-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. PCC 6803 (bacteria) / Plasmid: PET29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P73600
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS PH8.0, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→37 Å / Num. obs: 70481 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.1 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XL9

2xl9


Resolution: 1.93→37.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.287 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20318 3571 5.1 %RANDOM
Rwork0.16135 ---
obs0.16347 66822 95.98 %-
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: 13.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.93→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7316 0 20 1069 8405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227564
X-RAY DIFFRACTIONr_bond_other_d0.0010.025001
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.94910335
X-RAY DIFFRACTIONr_angle_other_deg0.8833.00112181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47924.586362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.413151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4741528
X-RAY DIFFRACTIONr_chiral_restr0.0870.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021552
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6761.54712
X-RAY DIFFRACTIONr_mcbond_other0.1881.51848
X-RAY DIFFRACTIONr_mcangle_it1.17727629
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06432852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2914.52706
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 244 -
Rwork0.17 4601 -
obs--91.66 %
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)
10.1899-0.0175-0.01740.2478-0.04760.1772-0.0069-0.0049-0.0088-0.0113-0.0018-0.0158-0.00370.00360.00870.00350.00640.00240.017-0.00030.0204-5.030712.1779-46.4851
20.1658-0.1125-0.01760.3353-0.00070.14760.00120.00950.01230.01160.01840.0198-0.01150.0136-0.01960.0120.01010.00370.01850.0080.0149-27.912639.1008-50.6006
30.1952-0.0928-0.06790.2837-0.00910.2058-0.0067-0.0121-0.0037-0.0118-0.00580.00780.01580.00860.01240.01280.01070.00070.01310.00680.013-17.569254.2497-18.5112
40.09580.0434-0.1080.476-0.14070.1711-0.0102-0.01730.015-0.11390.03930.01590.0508-0.0148-0.02910.0413-0.0256-0.01270.02880.00780.0083-8.152922.755416.2934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A65 - 297
2X-RAY DIFFRACTION2B64 - 297
3X-RAY DIFFRACTION3C63 - 297
4X-RAY DIFFRACTION4D64 - 297

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