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- PDB-2apj: X-Ray Structure of Protein from Arabidopsis Thaliana AT4G34215 at... -

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Basic information

Entry
Database: PDB / ID: 2apj
TitleX-Ray Structure of Protein from Arabidopsis Thaliana AT4G34215 at 1.6 Angstrom Resolution
ComponentsPutative Esterase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AT4G34215 / Putative Esterase / SGNH-HYDROLASE SUPERFAMILY / CARBOHYDRATE ESTERASE FAMILY 6 / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds / hydrolase activity / cytosol
Similarity search - Function
: / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable carbohydrate esterase At4g34215 / Probable carbohydrate esterase At4g34215
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bitto, E. / Bingman, C.A. / Allard, S.T. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana.
Authors: Bitto, E. / Bingman, C.A. / McCoy, J.G. / Allard, S.T. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionAug 16, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionAug 30, 2005ID: 2AEA
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Esterase
B: Putative Esterase
C: Putative Esterase
D: Putative Esterase


Theoretical massNumber of molelcules
Total (without water)114,1864
Polymers114,1864
Non-polymers00
Water29,0221611
1
A: Putative Esterase


Theoretical massNumber of molelcules
Total (without water)28,5461
Polymers28,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Esterase


Theoretical massNumber of molelcules
Total (without water)28,5461
Polymers28,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative Esterase


Theoretical massNumber of molelcules
Total (without water)28,5461
Polymers28,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative Esterase


Theoretical massNumber of molelcules
Total (without water)28,5461
Polymers28,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.688, 71.918, 93.213
Angle α, β, γ (deg.)108.16, 93.25, 90.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHEAA20 - 4020 - 40
21PROPROPHEPHEBB20 - 4020 - 40
31PROPROPHEPHECC20 - 4020 - 40
41PROPROPHEPHEDD20 - 4020 - 40
52TRPTRPASNASNAA50 - 10050 - 100
62TRPTRPASNASNBB50 - 10050 - 100
72TRPTRPASNASNCC50 - 10050 - 100
82TRPTRPASNASNDD50 - 10050 - 100
93SERSERCYSCYSAA110 - 260110 - 260
103SERSERCYSCYSBB110 - 260110 - 260
113SERSERCYSCYSCC110 - 260110 - 260
123SERSERCYSCYSDD110 - 260110 - 260

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Components

#1: Protein
Putative Esterase


Mass: 28546.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4G34215 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: O49483, UniProt: Q8L9J9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1611 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.346.8
22.346.8
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2772vapor diffusion, hanging drop5.5PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS-TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (17% PEG 4000, 0.020 M POTASSIUM NITRATE, 0.050 M MES, 0.050 M SODIUM ACETATE PH 5.5), vapor diffusion, hanging drop, temperature 277K
2731vapor diffusion, hanging drop5.5PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS-TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (18% PEG 4000, 0.010 M POTASSIUM NITRATE, 0.050 M MES, 0.050 M SODIUM ACETATE PH 5.5), vapor diffusion, hanging drop, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.98245
SYNCHROTRONAPS 22-ID20.97234
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDAug 10, 2005PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS
MARMOSAIC 225 mm CCD2CCDJul 10, 2005HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1INDIRECT LIQUID NITROGEN COOLED DOUBLE CRYSTAL MONOCHROMATOR WITH SI-111 CRYSTALSSINGLE WAVELENGTHMx-ray1
2WATER COOLED SI (111) DOUBLE BOUNCESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.982451
20.972341
Reflection

D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)% possible obs
3.811250430.0471.021.694.5
3.62298930.0711.0492.693.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.955099.110.031.0753.9
3.133.9598.810.0321.0864
2.743.1398.210.0421.0813.9
2.492.7497.810.0451.023.9
2.312.4997.510.0521.0443.9
2.172.319710.0561.0483.8
2.062.1796.110.0670.9743.8
1.972.0695.110.0771.0433.7
1.91.9794.210.0891.0193.7
1.831.993.710.1111.053.7
1.771.8393.210.1351.0053.7
1.721.7792.410.160.9713.7
1.681.729210.1920.9483.6
1.641.6889.110.220.9573.5
1.61.6483.710.240.9223.4
5.65099.720.0371.4484
4.455.699.420.0441.1344
3.884.4599.320.0561.0454
3.533.8899.220.0761.0734
3.283.5399.120.1120.963.9
3.083.2898.820.1960.9093.8
2.933.0898.520.2420.9063.5
2.82.9396.420.3180.9183.1
2.692.885.820.3810.9752.7
2.62.6962.120.4370.9092.3
ReflectionResolution: 1.6→50 Å / Num. obs: 125043 / % possible obs: 94.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Χ2: 1.02 / Net I/σ(I): 17.57
Reflection shellResolution: 1.6→1.64 Å / % possible obs: 83.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.611 / Num. measured obs: 7428 / Χ2: 0.922 / % possible all: 83.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.577 / Cor.coef. Fo:Fc: 0.274
Highest resolutionLowest resolution
Rotation3 Å47.27 Å
Translation3 Å47.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHYRE SERVER HOMOLOGY MODEL BASED ON 1ZMB

1zmb


Resolution: 1.6→35.852 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.153 / SU B: 2.813 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 6226 4.987 %RANDOM
Rwork0.1456 ---
all0.147 ---
obs0.14746 124841 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 8.471 Å2
Baniso -1Baniso -2Baniso -3
1-0.969 Å2-0.051 Å2-0.536 Å2
2---0.932 Å2-0.355 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7468 0 0 1611 9079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227675
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.96610415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92824.543339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.596151313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9541548
X-RAY DIFFRACTIONr_chiral_restr0.1220.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025779
X-RAY DIFFRACTIONr_nbd_refined0.2190.23975
X-RAY DIFFRACTIONr_nbtor_refined0.310.25372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.21320
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.2100
X-RAY DIFFRACTIONr_mcbond_it0.9941.54899
X-RAY DIFFRACTIONr_mcangle_it1.48127726
X-RAY DIFFRACTIONr_scbond_it2.60133110
X-RAY DIFFRACTIONr_scangle_it4.0294.52689
Refine LS restraints NCS

Ens-ID: 1 / Number: 1682 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDRmsTypeWeight
1A0.22MEDIUM POSITIONAL0.5
2B0.22MEDIUM POSITIONAL0.5
3C0.32MEDIUM POSITIONAL0.5
4D0.26MEDIUM POSITIONAL0.5
1A0.88MEDIUM THERMAL2
2B0.95MEDIUM THERMAL2
3C1.03MEDIUM THERMAL2
4D1.14MEDIUM THERMAL2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6410.2384200.197638978182.384
1.641-1.6860.2294260.1798076950889.419
1.686-1.7350.2074110.178066921192.031
1.735-1.7880.2044380.1577971907992.62
1.788-1.8470.2043590.1547778874193.09
1.847-1.9120.1813970.1487462836993.906
1.912-1.9840.1634260.1447233811994.334
1.984-2.0640.1763640.1487129785595.391
2.064-2.1560.1693450.1466874752395.959
2.156-2.2610.1923500.1396620720796.712
2.261-2.3820.2023540.1416303682397.567
2.382-2.5260.1993090.1456012647297.667
2.526-2.70.1882940.1435599602697.793
2.7-2.9140.1782800.1445288568297.994
2.914-3.1910.172530.1444854518798.458
3.191-3.5640.1612270.1284417470398.745
3.564-4.1080.152080.1243924417598.97
4.108-5.0150.1671670.1273310350799.145
5.015-7.0240.2231140.1842607273699.452
7.024-35.8520.197840.1671454155798.78
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)
10.87120.03680.21671.2323-0.05271.0523-0.0038-0.03630.0270.03640.0418-0.03750.06060.0288-0.038-0.21260.00390.0038-0.1586-0.0006-0.15981.0080.8410.064
20.82540.043-0.1981.1852-0.01691.21960.0242-0.0059-0.01020.02330.0238-0.04-0.07830.0323-0.048-0.2008-0.003-0.0047-0.1596-0.0034-0.138921.32828.49815.447
31.15530.15790.851.38350.38821.79460.024-0.03050.0010.0197-0.02080.039-0.047-0.0054-0.0032-0.04590.0371-0.0216-0.1335-0.0003-0.160118.68658.3541.983
40.71860.0878-0.30561.90510.55111.52390.03410.0567-0.0134-0.17860.0127-0.0484-0.04080.102-0.0467-0.0713-0.0216-0.0079-0.1151-0.0047-0.1499-2.21-28.557-26.769
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA17 - 26017 - 260
22BB18 - 26018 - 260
33CC20 - 26020 - 260
44DD20 - 26020 - 260

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