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- PDB-5j7m: Crystal structure of Cupin 2 conserved barrel domain protein from... -

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Basic information

Entry
Database: PDB / ID: 5j7m
TitleCrystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM 17836
ComponentsCupin 2 conserved barrel domain protein
KeywordsUNKNOWN FUNCTION / Cupin 2 conserved barrel domain
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 / ETHANOL / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsChang, C. / Cuff, M. / Chhor, G. / Endres, M. / Joachimiak, A.
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: Crystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM 17836
Authors: Chang, C. / Cuff, M. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references / Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 23, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,82011
Polymers27,1272
Non-polymers6939
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-51 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.162, 61.162, 120.973
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cupin 2 conserved barrel domain protein


Mass: 13563.562 Da / Num. of mol.: 2 / Fragment: residues 1-120
Source method: isolated from a genetically manipulated source
Details: N-terminal cloning artifact SNA / Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_2934
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D2Q1L0

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Non-polymers , 5 types, 79 molecules

#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Magnesium chloride, HEPES, ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791833 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791833 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 15720 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 23.87 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 0.941 / Net I/av σ(I): 16.252 / Net I/σ(I): 9.8 / Num. measured all: 97051
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.07-2.114.90.7221100
2.11-2.145.10.6661100
2.14-2.195.50.5361100
2.19-2.235.80.5261100
2.23-2.2860.4551100
2.28-2.3360.4431100
2.33-2.3960.3851100
2.39-2.456.10.3321100
2.45-2.536.10.2941100
2.53-2.616.10.241199.9
2.61-2.76.20.2199.7
2.7-2.816.30.17199.7
2.81-2.946.30.139199.8
2.94-3.096.50.106199.7
3.09-3.296.70.076199.7
3.29-3.546.70.066199.6
3.54-3.96.90.057199.5
3.9-4.466.90.047198.5
4.46-5.626.90.042197.1
5.62-506.70.051195.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(dev_2328)refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→39.849 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.224 1441 5.34 %
Rwork0.1796 --
obs0.1822 15017 86.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.04 Å2 / Biso mean: 29.7677 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 2.07→39.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 40 70 1979
Biso mean--41.66 31.51 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071952
X-RAY DIFFRACTIONf_angle_d0.9452664
X-RAY DIFFRACTIONf_chiral_restr0.056302
X-RAY DIFFRACTIONf_plane_restr0.006345
X-RAY DIFFRACTIONf_dihedral_angle_d13.7491125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0613-2.1350.2755770.22511411148848
2.135-2.22050.28631000.22151959205966
2.2205-2.32150.28091120.22242542265485
2.3215-2.44390.27131430.22842792293593
2.4439-2.5970.35421430.21482806294995
2.597-2.79750.25911120.2212872298495
2.7975-3.07890.2481630.20392791295495
3.0789-3.52420.23422000.16632762296295
3.5242-4.43920.20171970.14532801299896
4.4392-39.8560.1641940.14462788298295
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)
10.1201-0.1549-0.03040.20860.0540.01780.0959-0.04040.043-0.01720.0746-0.02390.1251-0.025300.14570.0032-0.00840.1960.02440.18512.694326.96420.591
20.1041-0.10580.04310.1289-0.11380.12740.00810.15110.22380.00510.0416-0.0885-0.1363-0.0936-00.1731-0.0076-0.01560.1417-0.00960.19888.817331.5628-0.8844
30.1232-0.0623-0.10860.02670.05440.09340.01420.24330.1479-0.0359-0.06180.05620.10980.0375-00.1743-0.0098-0.02250.16330.0430.17639.528224.3697-14.2193
40.10880.10580.02550.1040.02630.0469-0.02810.18360.3418-0.0673-0.1341-0.1079-0.15040.0077-0.01610.25160.08070.03990.180.08730.212114.748718.7684-21.2362
50.1917-0.2341-0.09280.26750.09750.03810.16940.11880.1676-0.1276-0.1353-0.43750.16910.26350.01030.17910.0519-0.01360.14090.0540.169714.479424.0136-14.7158
60.01060.00880.02280.0204-0.00170.0905-0.08490.0071-0.38450.08260.05510.09240.16310.02640.0010.2217-0.0089-0.00340.10450.00780.33832.760112.2829-13.187
70.0317-0.0248-0.03140.02060.00630.06180.00040.14950.07340.0235-0.0822-0.00760.0321-0.113900.1857-0.017-0.00920.13510.03170.160312.605328.7865-7.1051
80.0799-0.050.0410.31590.26980.3140.1059-0.06440.0170.0124-0.0462-0.1053-0.22620.16510.1050.3156-0.2787-0.01240.4858-0.08450.223627.284940.2102-4.844
90.05910.0408-0.0420.0248-0.02580.02340.05440.24270.1093-0.024-0.0631-0.23340.06930.13440.00010.24850.05990.01950.2410.03560.234123.79617.5833-10.8787
100.0415-0.0030.10970.15860.0030.51370.1417-0.06720.14350.0475-0.07140.01090.17890.0360.00310.0506-0.0007-0.03540.1670.05740.189127.571420.0309-1.509
110.0173-0.01090.01670.0066-0.01030.01510.0463-0.0470.2293-0.163-0.05460.00530.04480.13870.00010.16770.0269-0.03730.17010.0460.237523.035418.54142.0581
120.0302-0.0122-0.02750.03090.03920.0621-0.0335-0.31740.0264-0.08980.0365-0.1403-0.0456-0.12420.00010.1506-0.0032-0.06580.1491-0.00440.195321.247220.00499.6012
130.089-0.04940.06490.0384-0.0360.0553-0.0408-0.2079-0.18330.1869-0.07180.01710.1016-0.1573-0.01560.18350.005-0.03320.3394-0.00870.137112.269318.67314.6335
140.3292-0.09640.16080.09610.02570.189-0.155-0.43770.07480.03770.28740.02470.11050.00210.13950.1262-0.0277-0.11820.2896-0.0615-0.058416.944223.57811.1094
150.0130.0038-0.0180.009-0.00490.01760.0950.2007-0.1317-0.11530.07560.16860.155-0.10720.00010.21-0.0063-0.02360.2280.0350.206513.5126.85599.7121
160.63180.0703-0.13520.2129-0.00110.0387-0.0075-0.03480.2127-0.10790.0059-0.07380.04640.12750.03080.13830.0005-0.03320.12140.02440.101821.358524.27263.2608
170.03690.0513-0.02660.0747-0.03740.0150.0459-0.0589-0.01830.0998-0.0599-0.1168-0.05640.01070.03930.5889-0.0620.05670.1586-0.0690.401821.680942.71510.6421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 19 )A-1 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 40 )A20 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 68 )A41 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 75 )A69 - 75
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 92 )A76 - 92
6X-RAY DIFFRACTION6chain 'A' and (resid 93 through 99 )A93 - 99
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 108 )A100 - 108
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 120 )A109 - 120
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 11 )B-1 - 11
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 33 )B12 - 33
11X-RAY DIFFRACTION11chain 'B' and (resid 34 through 40 )B34 - 40
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 61 )B41 - 61
13X-RAY DIFFRACTION13chain 'B' and (resid 62 through 76 )B62 - 76
14X-RAY DIFFRACTION14chain 'B' and (resid 77 through 92 )B77 - 92
15X-RAY DIFFRACTION15chain 'B' and (resid 93 through 99 )B93 - 99
16X-RAY DIFFRACTION16chain 'B' and (resid 100 through 108 )B100 - 108
17X-RAY DIFFRACTION17chain 'B' and (resid 109 through 120 )B109 - 120

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