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- PDB-2odf: The crystal structure of gene product Atu2144 from Agrobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2odf
TitleThe crystal structure of gene product Atu2144 from Agrobacterium tumefaciens
ComponentsHypothetical protein Atu2144
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyUncharacterised conserved protein UCP029730 / N-formylglutamate amidohydrolase / N-formylglutamate amidohydrolase / Zn-dependent exopeptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / N-formylglutamate amidohydrolase / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of gene product Atu2144 from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Hypothetical protein Atu2144
B: Hypothetical protein Atu2144
C: Hypothetical protein Atu2144
D: Hypothetical protein Atu2144
E: Hypothetical protein Atu2144
F: Hypothetical protein Atu2144
G: Hypothetical protein Atu2144
H: Hypothetical protein Atu2144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,75918
Polymers224,7988
Non-polymers96110
Water29,0581613
1
A: Hypothetical protein Atu2144
D: Hypothetical protein Atu2144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4885
Polymers56,1992
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-47 kcal/mol
Surface area21500 Å2
MethodPISA
2
B: Hypothetical protein Atu2144
F: Hypothetical protein Atu2144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4885
Polymers56,1992
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-48 kcal/mol
Surface area21050 Å2
MethodPISA
3
C: Hypothetical protein Atu2144
H: Hypothetical protein Atu2144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4885
Polymers56,1992
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-49 kcal/mol
Surface area21230 Å2
MethodPISA
4
E: Hypothetical protein Atu2144
G: Hypothetical protein Atu2144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2963
Polymers56,1992
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-29 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.523, 89.765, 120.365
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein exists as monomer. There are 8 molecules (A,B,C,D,E,F,G,H) in the asymmetric unit.

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Components

#1: Protein
Hypothetical protein Atu2144 / AGR_C_3887p


Mass: 28099.748 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8UDI1, UniProt: A9CI91*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1613 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% Isopropanol, 2M Ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→120 Å / Num. all: 175032 / Num. obs: 173247 / % possible obs: 98.98 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22
Reflection shellResolution: 1.9→1.952 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Num. unique all: 13470 / % possible all: 95.72

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→120 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.71 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23394 9148 5 %RANDOM
Rwork0.18891 ---
obs0.19113 173247 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.43 Å2
2---1.25 Å20 Å2
3---1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.036 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.9→120 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15391 0 50 1613 17054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02115745
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210511
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.96221386
X-RAY DIFFRACTIONr_angle_other_deg0.939325521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95651997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11923.338731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.397152502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01715132
X-RAY DIFFRACTIONr_chiral_restr0.0790.22409
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023251
X-RAY DIFFRACTIONr_nbd_refined0.2190.23606
X-RAY DIFFRACTIONr_nbd_other0.2030.211558
X-RAY DIFFRACTIONr_nbtor_refined0.1720.27746
X-RAY DIFFRACTIONr_nbtor_other0.0850.28199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.21261
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.255
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.2212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.270
X-RAY DIFFRACTIONr_mcbond_it1.0721.512781
X-RAY DIFFRACTIONr_mcbond_other0.161.54051
X-RAY DIFFRACTIONr_mcangle_it1.166215969
X-RAY DIFFRACTIONr_scbond_it2.01536485
X-RAY DIFFRACTIONr_scangle_it2.8894.55417
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 663 -
Rwork0.253 12231 -
obs-12231 95.72 %
Refinement TLS params.Method: refined / Origin x: 25.685 Å / Origin y: 51.935 Å / Origin z: 23.625 Å
111213212223313233
T-0.0041 Å2-0.0171 Å20.0165 Å2--0.0185 Å20.0014 Å2--0.0324 Å2
L0.009 °2-0.0164 °2-0.0007 °2-0.0298 °20.0001 °2--0.0282 °2
S0.004 Å °0.0077 Å °0.0156 Å °-0.0044 Å °0.0019 Å °-0.0053 Å °0.0111 Å °0.0088 Å °-0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 80
2X-RAY DIFFRACTION1A81 - 160
3X-RAY DIFFRACTION1A161 - 257
4X-RAY DIFFRACTION1B2 - 80
5X-RAY DIFFRACTION1B81 - 160
6X-RAY DIFFRACTION1B164 - 256
7X-RAY DIFFRACTION1C7 - 80
8X-RAY DIFFRACTION1C81 - 160
9X-RAY DIFFRACTION1C161 - 255
10X-RAY DIFFRACTION1D7 - 80
11X-RAY DIFFRACTION1D81 - 160
12X-RAY DIFFRACTION1D161 - 256
13X-RAY DIFFRACTION1E6 - 80
14X-RAY DIFFRACTION1E81 - 160
15X-RAY DIFFRACTION1E161 - 256
16X-RAY DIFFRACTION1F6 - 80
17X-RAY DIFFRACTION1F81 - 160
18X-RAY DIFFRACTION1F161 - 256
19X-RAY DIFFRACTION1G7 - 80
20X-RAY DIFFRACTION1G81 - 160
21X-RAY DIFFRACTION1G161 - 256
22X-RAY DIFFRACTION1H6 - 80
23X-RAY DIFFRACTION1H81 - 160
24X-RAY DIFFRACTION1H161 - 256

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