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- PDB-1vqy: CRYSTAL STRUCTURE OF a NIPSNAP FAMILY PROTEIN (ATU5224) FROM AGRO... -

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Basic information

Entry
Database: PDB / ID: 1vqy
TitleCRYSTAL STRUCTURE OF a NIPSNAP FAMILY PROTEIN (ATU5224) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 2.40 A RESOLUTION
Componentshypothetical protein AGR_pAT_315
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


NIPSNAP / NIPSNAP / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / NIPSNAP domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (np_396154.1) from Agrobacterium tumefaciens at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: hypothetical protein AGR_pAT_315
B: hypothetical protein AGR_pAT_315
C: hypothetical protein AGR_pAT_315
D: hypothetical protein AGR_pAT_315
E: hypothetical protein AGR_pAT_315
F: hypothetical protein AGR_pAT_315
G: hypothetical protein AGR_pAT_315
H: hypothetical protein AGR_pAT_315
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6409
Polymers109,5458
Non-polymers951
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18210 Å2
ΔGint-108 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.035, 110.924, 129.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 104 / Label seq-ID: 13 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
hypothetical protein AGR_pAT_315


Mass: 13693.145 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Gene: AGR_pAT_315 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UK99, UniProt: A9CLJ4*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.4 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 15% PEG MME 5000, 0.06M Tris Cl, 0.04M Tris_base, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.110.979625
SYNCHROTRONALS 8.3.120.979625,0.979741,1.019951
DetectorType: ADSC / Detector: CCD / Date: Oct 9, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796251
20.9797411
31.0199511
ReflectionResolution: 2.4→29.28 Å / Num. obs: 38294 / % possible obs: 98 % / Redundancy: 6.1 % / Biso Wilson estimate: 34.74 Å2 / Rsym value: 0.153 / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2768 / Rsym value: 0.325 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.08 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.884 / SU B: 15.682 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.269
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24436 1913 5 %RANDOM
Rwork0.18633 ---
obs0.18932 36309 97.55 %-
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: 19.119 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1.52 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6798 0 5 480 7283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226936
X-RAY DIFFRACTIONr_bond_other_d0.0010.026657
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9789374
X-RAY DIFFRACTIONr_angle_other_deg0.825315321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60722.562320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.744151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2651576
X-RAY DIFFRACTIONr_chiral_restr0.0730.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021459
X-RAY DIFFRACTIONr_nbd_refined0.1950.21297
X-RAY DIFFRACTIONr_nbd_other0.1820.26774
X-RAY DIFFRACTIONr_nbtor_other0.0810.24333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2350
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.213
X-RAY DIFFRACTIONr_mcbond_it1.55334626
X-RAY DIFFRACTIONr_mcbond_other0.40631734
X-RAY DIFFRACTIONr_mcangle_it1.7656790
X-RAY DIFFRACTIONr_scbond_it3.28482997
X-RAY DIFFRACTIONr_scangle_it4.421112584
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23285
Refine LS restraints NCS

Ens-ID: 1 / Number: 1618 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.470.5
2Bmedium positional0.440.5
3Cmedium positional0.30.5
4Dmedium positional0.450.5
5Emedium positional0.350.5
6Fmedium positional0.350.5
7Gmedium positional0.320.5
8Hmedium positional0.390.5
1Amedium thermal0.612
2Bmedium thermal0.612
3Cmedium thermal0.622
4Dmedium thermal0.672
5Emedium thermal0.632
6Fmedium thermal0.642
7Gmedium thermal0.582
8Hmedium thermal0.652
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 132 4.82 %
Rwork0.226 2608 -
obs--96.34 %
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)
11.30980.70040.48932.19580.43340.99650.0783-0.0337-0.1463-0.0407-0.0121-0.20190.19020.1796-0.06620.0031-0.0005-0.008-0.0220.0075-0.0294139.633141.243830.445
20.55180.334-0.18121.2811-0.26110.54210.0639-0.04490.03990.0449-0.00380.1435-0.0736-0.1399-0.0601-0.0436-0.00730.0039-0.00910.0083-0.051100.731252.650930.8529
31.34690.78630.06751.0709-0.01421.1764-0.04960.0574-0.0142-0.1109-0.0238-0.04370.0005-0.01520.0733-0.07040.00640.0128-0.0407-0.0004-0.072119.737748.52310.8263
40.86870.14830.11022.2380.51950.8162-0.001-0.1987-0.18390.145-0.0139-0.20260.0865-0.03960.015-0.0205-0.0027-0.0063-0.01530.0357-0.0475119.802145.892550.4514
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 10412 - 116
21BB-9 - 1043 - 116
32CC0 - 10412 - 116
42DD1 - 10413 - 116
53EE1 - 10413 - 116
63FF0 - 10412 - 116
74GG0 - 10412 - 116
84HH0 - 10412 - 116

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