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Basic information

Entry
Database: PDB / ID: 4had
TitleCrystal structure of probable oxidoreductase protein from Rhizobium etli CFN 42
ComponentsProbable oxidoreductase protein
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


: / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable oxidoreductase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of probable oxidoreductase protein from Rhizobium etli CFN 42
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionSep 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / 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_asym_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_label_asym_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_asym_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Probable oxidoreductase protein
B: Probable oxidoreductase protein
C: Probable oxidoreductase protein
D: Probable oxidoreductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2648
Polymers159,1734
Non-polymers924
Water15,799877
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-58 kcal/mol
Surface area45180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.662, 160.081, 192.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 0 - 328 / Label seq-ID: 22 - 350

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Probable oxidoreductase protein


Mass: 39793.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: RHE_CH00272 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q2KDJ1
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17M ammonium acetate, 0.085 M sodium citrate-HCl, pH 5.6, 25.5% PEG4000, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 13.02 / Number: 618604 / Rmerge(I) obs: 0.132 / Χ2: 1.93 / D res high: 2 Å / D res low: 50 Å / Num. obs: 180659 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.435099.910.0472.0513.9
4.315.4399.810.0572.593.7
3.764.3199.810.072.9243.6
3.423.7699.510.0852.8823.5
3.173.4299.210.1022.4593.5
2.993.179910.1272.2993.5
2.842.9998.910.1542.1073.4
2.712.8498.610.1881.9563.4
2.612.7198.710.2181.8733.4
2.522.6198.410.2691.7573.4
2.442.529810.2911.723.4
2.372.4497.910.3441.6453.3
2.312.3797.810.3651.5983.3
2.252.3197.110.3981.5883.3
2.22.2597.410.4411.5293.3
2.152.297.210.5151.5143.3
2.112.1597.110.6191.4313.3
2.072.119710.6591.4273.3
2.032.0797.110.7361.3883.3
22.0397.310.8681.3433.3
ReflectionResolution: 2→50 Å / Num. obs: 180659 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.132 / Χ2: 1.933 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.30.86888981.343197.3
2.03-2.073.30.73690421.388197.1
2.07-2.113.30.65987921.427197
2.11-2.153.30.61989471.431197.1
2.15-2.23.30.51589141.514197.2
2.2-2.253.30.44189601.529197.4
2.25-2.313.30.39889341.588197.1
2.31-2.373.30.36589551.598197.8
2.37-2.443.30.34490251.645197.9
2.44-2.523.40.29190451.72198
2.52-2.613.40.26989641.757198.4
2.61-2.713.40.21891271.873198.7
2.71-2.843.40.18890871.956198.6
2.84-2.993.40.15490412.107198.9
2.99-3.173.50.12790762.299199
3.17-3.423.50.10291282.459199.2
3.42-3.763.50.08591762.882199.5
3.76-4.313.60.0791372.924199.8
4.31-5.433.70.05791752.59199.8
5.43-503.90.04792362.051199.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2006 / WRfactor Rwork: 0.1703 / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.8565 / SU B: 8.108 / SU ML: 0.114 / SU R Cruickshank DPI: 0.1731 / SU Rfree: 0.1462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 4762 5 %RANDOM
Rwork0.1748 ---
obs0.1763 95313 98.75 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 163.7 Å2 / Biso mean: 32.9759 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0 Å2-0 Å2
2--1.84 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10034 0 4 877 10915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910293
X-RAY DIFFRACTIONr_bond_other_d0.0050.029678
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.94913949
X-RAY DIFFRACTIONr_angle_other_deg1.034322209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91951280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28423.537523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.754151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8551597
X-RAY DIFFRACTIONr_chiral_restr0.0750.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211820
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022461
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A199890.06
12B199890.06
21A199500.07
22C199500.07
31A200130.07
32D200130.07
41B198130.07
42C198130.07
51B199710.06
52D199710.06
61C198930.07
62D198930.07
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 346 -
Rwork0.256 6506 -
all-6852 -
obs--97.12 %
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)
10.2802-0.26620.09231.17230.61.1430.08560.1880.0559-0.1833-0.1033-0.11780.07870.03630.01780.17590.04190.0350.150.05350.157234.61482.04893.4
20.4707-0.16640.31121.23660.4271.39640.0236-0.0385-0.1514-0.0359-0.01910.02510.3258-0.0297-0.00460.21120.00920.00360.0120.04380.201739.83260.229121.559
30.5859-0.2947-0.08451.10510.29691.2617-0.03090.0420.37330.1046-0.0323-0.2353-0.33530.00340.06330.23-0.0165-0.04810.00630.04590.41341.749114.698118.901
40.6879-0.08740.05921.08510.32371.0814-0.1076-0.27880.15130.23630.0759-0.1406-0.1411-0.05510.03180.2040.0521-0.04920.1275-0.03340.177733.25593.344146.641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 328
2X-RAY DIFFRACTION2B0 - 328
3X-RAY DIFFRACTION3C0 - 328
4X-RAY DIFFRACTION4D0 - 328

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