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- PDB-5uqp: The crystal structure of cupin protein from Rhodococcus jostii RHA1 -

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Basic information

Entry
Database: PDB / ID: 5uqp
TitleThe crystal structure of cupin protein from Rhodococcus jostii RHA1
ComponentsCupin
KeywordsUNKNOWN FUNCTION / CUPIN protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin_2 domain-containing protein
Function and homology information
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTan, K. / Li, H. / Clancy, S. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: The crystal structure of cupin protein from Rhodococcus jostii RHA1
Authors: Tan, K. / Li, H. / Clancy, S. / Phillips Jr., G.N. / Joachimiak, A.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cupin
B: Cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0868
Polymers27,7532
Non-polymers3336
Water1,56787
1
A: Cupin
B: Cupin
hetero molecules

A: Cupin
B: Cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,17216
Polymers55,5064
Non-polymers66612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area13440 Å2
ΔGint-316 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.448, 139.448, 80.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Cupin


Mass: 13876.456 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (strain RHA1) (bacteria)
Strain: RHA1 / Gene: RHA1_ro08652 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q0RYE0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium Iodide, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2016 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18365 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.021 / Χ2: 0.991 / Net I/σ(I): 32.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 20 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 899 / CC1/2: 0.95 / Rpim(I) all: 0.194 / Χ2: 0.911 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.212 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.66
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 943 5.13 %random
Rwork0.1659 ---
obs0.1677 18365 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 10 88 1850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151802
X-RAY DIFFRACTIONf_angle_d1.3252457
X-RAY DIFFRACTIONf_dihedral_angle_d8.951057
X-RAY DIFFRACTIONf_chiral_restr0.085267
X-RAY DIFFRACTIONf_plane_restr0.008322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.52660.29471370.20992367X-RAY DIFFRACTION98
2.5266-2.68490.23761390.19072452X-RAY DIFFRACTION100
2.6849-2.89210.2261260.17872446X-RAY DIFFRACTION100
2.8921-3.18310.20831190.17212487X-RAY DIFFRACTION100
3.1831-3.64360.17421250.15382494X-RAY DIFFRACTION100
3.6436-4.590.17791480.13962509X-RAY DIFFRACTION100
4.59-48.22140.18921490.17182667X-RAY DIFFRACTION100
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)
12.02093.5233-2.25998.3946-4.60032.7482-0.56340.8392-0.874-0.60520.1649-0.56141.49590.19560.19730.72880.1524-0.06740.66-0.21250.475138.840544.5471-15.9086
28.28137.0338-6.6416.1781-5.06836.962-0.1712-0.13170.5756-0.28490.27320.247-0.163-0.4933-0.14870.42950.2607-0.01110.5801-0.06980.309350.401158.9771-23.8667
33.0123-3.3079-2.20094.28511.85191.98010.15710.929-1.00090.1209-0.23740.55580.43850.20360.1490.3550.2502-0.12010.5511-0.15860.318731.788753.7636-16.6202
49.0677-0.9269-6.43031.5310.75344.63520.09640.5659-0.3333-0.1096-0.2110.35550.3244-0.28860.12080.23410.077-0.02920.2297-0.04590.220610.09566.497-7.4602
59.20280.0088-3.14051.82130.94073.9934-0.8648-0.6816-0.63610.70860.11750.33530.78730.26670.58130.37480.02610.07260.2187-0.00870.37185.401562.09295.583
62.3305-2.2785-0.97694.19681.5220.63420.37350.3459-0.0362-0.2328-0.13030.2240.34970.1839-0.13350.18060.0563-0.04790.28430.0160.17959.365671.79990.2082
77.8726-5.51993.73338.9404-3.8955.9047-0.1448-0.4909-0.37950.4290.21340.18160.02990.1613-0.12870.17930.04010.02820.19280.01330.21673.406372.858811.1288
83.4154-1.718-0.45892.16210.25081.6948-0.2519-0.4702-0.1250.30740.2309-0.04250.2670.28610.01940.26170.10620.00140.3223-0.00220.167410.098768.73497.1121
91.32230.6292-1.5281.9126-0.10794.52590.16310.18440.12040.0338-0.04260.15720.1508-0.0104-0.0550.1573-0.0062-0.04410.1423-0.01810.17285.884369.0039-0.362
106.14587.173-5.63549.647-7.49095.8445-0.9251.90360.3171-1.76430.90880.45621.7253-1.40770.15630.5529-0.0583-0.07920.6378-0.07750.31457.732570.3679-22.6621
116.68055.7151-5.55357.2587-7.3477.4836-0.84020.3479-0.5546-0.327-0.22560.46612.106-0.24930.44840.4865-0.05130.10520.227-0.07150.4856-0.789260.1941-5.2251
123.702-2.4556-5.19352.26142.92037.63760.06250.7578-0.40850.1146-0.08210.02830.3748-0.36080.15530.31850.0588-0.09830.3121-0.04440.310110.016663.0354-12.812
136.6911-0.9598-1.23990.5020.33460.50130.3620.22960.6308-0.5777-0.1334-0.1782-0.53170.0914-0.08330.32660.3047-0.0970.6312-0.06550.306244.432362.3837-15.7842
143.7447-3.4294-1.30093.19291.22850.6981-0.2517-0.12750.0584-0.1237-0.09690.0927-0.16910.4133-0.39580.26170.38380.02660.7225-0.18150.291847.929161.314-8.1135
153.19640.1507-1.14252.40510.07751.8365-0.112-0.64470.9541-0.00740.2844-0.3351-0.27770.523-0.11590.31680.225-0.07920.6952-0.19550.476352.158565.7847-9.9493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 54 )
5X-RAY DIFFRACTION5chain 'A' and (resid 55 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 90 )
8X-RAY DIFFRACTION8chain 'A' and (resid 91 through 106 )
9X-RAY DIFFRACTION9chain 'A' and (resid 107 through 122 )
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 20 )
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 30 )
12X-RAY DIFFRACTION12chain 'B' and (resid 31 through 40 )
13X-RAY DIFFRACTION13chain 'B' and (resid 41 through 67 )
14X-RAY DIFFRACTION14chain 'B' and (resid 68 through 75 )
15X-RAY DIFFRACTION15chain 'B' and (resid 76 through 122 )

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