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- PDB-3c0v: Crystal structure of cytokinin-specific binding protein in comple... -

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Basic information

Entry
Database: PDB / ID: 3c0v
TitleCrystal structure of cytokinin-specific binding protein in complex with cytokinin and Ta6Br12
ComponentsCytokinin-specific binding protein
KeywordsPLANT PROTEIN / MAD / Ta6Br12 complex / CYTOKININS / ZEATIN / PATHOGENESIS-RELATED PROTEINS / Plant defense
Function / homology
Function and homology information


gibberellin binding / cytokinin binding / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / Phytohormone-binding protein CSBP / Phytohormone-binding protein CSBP
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPasternak, O. / Bujacz, A. / Biesiadka, J. / Bujacz, G. / Sikorski, M. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: MAD phasing using the (Ta(6)Br(12))(2+) cluster: a retrospective study
Authors: Pasternak, O. / Bujacz, A. / Biesiadka, J. / Bujacz, G. / Sikorski, M. / Jaskolski, M.
#1: Journal: Plant Cell / Year: 2006
Title: Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_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: Cytokinin-specific binding protein
B: Cytokinin-specific binding protein
C: Cytokinin-specific binding protein
D: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,27418
Polymers70,4514
Non-polymers11,82214
Water10,413578
1
A: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3796
Polymers17,6131
Non-polymers4,7665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0744
Polymers17,6131
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7254
Polymers17,6131
Non-polymers4,1123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0964
Polymers17,6131
Non-polymers2,4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Cytokinin-specific binding protein
C: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7998
Polymers35,2262
Non-polymers4,5746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-33 kcal/mol
Surface area14620 Å2
MethodPISA
6
A: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3796
Polymers17,6131
Non-polymers4,7665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0964
Polymers17,6131
Non-polymers2,4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.219, 113.219, 85.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytokinin-specific binding protein


Mass: 17612.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: VrCSBP / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ZWP8, UniProt: A0A1S3THR8*PLUS

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Non-polymers , 5 types, 592 molecules

#2: Chemical
ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN / Zeatin


Mass: 219.243 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O
#3: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br12Ta6
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO AUTHORS, THERE IS AN ERROR IN THE UNIPROTKB ENTRY UNP Q9ZWP8 AT POSITION 92 (ASN INSTEAD OF SER).

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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: 2.23 Å3/Da / Density % sol: 44.95 % / Description: THE STRUCTURE FACTOR FILE CONTAINS MAD SETS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M SODIUM CITRATE, 0.1M HEPES, pH 7.5,3mM ZEATIN, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.2547, 1.2580, 1.2703
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 23, 2005 / Details: monochromator
RadiationMonochromator: fixed exit double crystal Si 111, horizontally focussing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25471
21.2581
31.27031
ReflectionResolution: 1.8→30 Å / Num. all: 57463 / Num. obs: 56873 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 55.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 5.5 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345softwaredata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.31 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.832 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20729 1160 2.1 %RANDOM
Rwork0.15796 ---
obs0.15897 55374 98.47 %-
all-57463 --
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: 29.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.55 Å20 Å2
2---1.1 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 203 578 5657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225334
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.762.0357216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29825.238231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16915963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8681521
X-RAY DIFFRACTIONr_chiral_restr0.1230.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023761
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.22521
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23581
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2590
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.2124
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.53027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8624988
X-RAY DIFFRACTIONr_scbond_it2.85732446
X-RAY DIFFRACTIONr_scangle_it4.5864.52107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 81 -
Rwork0.182 3873 -
obs--94.03 %
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)
11.7756-0.8105-0.13272.0858-0.0930.9123-0.0791-0.1454-0.03810.04230.084-0.00160.0047-0.0619-0.0048-0.0709-0.001-0.0053-0.07090.0155-0.141330.7143-15.02432.0425
21.376-0.9327-0.32414.693-0.39962.37680.08750.0977-0.122-0.5028-0.01580.1790.1331-0.1379-0.0717-0.0553-0.0114-0.0359-0.0365-0.0023-0.167733.6567-17.7376-7.211
31.3942-0.1633-0.05312.50140.17310.4795-0.0166-0.1857-0.03240.03050.00680.19560.0534-0.01780.0098-0.079-0.00680.0018-0.04650.0075-0.152325.533414.02392.2555
41.75210.78840.23833.1293-0.34560.3740.03830.05040.0918-0.25670.01690.26660.04720.0094-0.0552-0.06660.012-0.0281-0.0569-0.0021-0.124923.936717.3511-6.5683
52.08810.5561-0.15020.5856-0.29170.86990.0088-0.1076-0.0588-0.0102-0.0814-0.0594-0.0843-0.04260.0726-0.05160.0005-0.0099-0.0752-0.0215-0.080655.532933.64472.5415
62.92951.886-1.38031.6926-0.87830.6517-0.13720.0274-0.26-0.12930.0204-0.10740.0031-0.08390.1168-0.0088-0.0178-0.0301-0.04760.0033-0.054157.95829.492-5.8893
71.6421-0.40090.14562.71290.18881.04650.0601-0.08120.0321-0.0821-0.0107-0.00340.043-0.0189-0.0494-0.0586-0.01530.0046-0.07590.0121-0.113354.830662.37892.6637
84.35132.69191.31314.94950.25530.4907-0.06570.32720.0461-0.47840.1728-0.0172-0.03140.1871-0.10710.04110.0042-0.0027-0.0299-0.0007-0.089653.238365.8789-6.2364
91.9522-1.4802-4.21381.30524.072613.3076-0.2114-0.04070.09290.31590.04070.56520.0802-0.04110.17070.14160.0004-0.00870.15510.0310.309911.1863-8.2224-1.9938
101.0575-1.1842-2.51941.32622.82146.0023-0.13650.37010.50780.06650.16870.56-0.1328-0.2053-0.03210.24490.0101-0.00970.1790.0190.323136.822542.5917-2.8223
110.9963-0.32411.39530.1054-0.45391.9541-0.0630.8059-0.0915-1.2210.2074-0.817-0.1966-0.2198-0.14440.3064-0.0255-0.04860.29780.02810.345815.0646-6.291-10.5746
124.2973-6.00343.71398.387-5.18843.2097-0.4519-0.50120.22560.5290.56080.5471-0.2058-0.5821-0.10880.3099-0.00250.01820.2586-0.03410.311745.008865.400915.5976
135.8673-2.503-5.63961.46870.583613.70380.08370.055-0.05040.4082-0.0863-0.1795-0.5074-0.18760.00260.33920.0205-0.00620.2970.04660.348564.472730.884815.7261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1251 - 125
2X-RAY DIFFRACTION2AA126 - 151126 - 151
3X-RAY DIFFRACTION3BB1 - 1251 - 125
4X-RAY DIFFRACTION4BB126 - 151126 - 151
5X-RAY DIFFRACTION5CC1 - 1251 - 125
6X-RAY DIFFRACTION6CC126 - 151126 - 151
7X-RAY DIFFRACTION7DD1 - 1251 - 125
8X-RAY DIFFRACTION8DD126 - 152126 - 152
9X-RAY DIFFRACTION9AM1581
10X-RAY DIFFRACTION10CN1571
11X-RAY DIFFRACTION11AO1591
12X-RAY DIFFRACTION12DP1581
13X-RAY DIFFRACTION13CQ1581

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