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- PDB-2aif: Crystal Structure of High Mobility Like Protein, NHP2, putative f... -

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Basic information

Entry
Database: PDB / ID: 2aif
TitleCrystal Structure of High Mobility Like Protein, NHP2, putative from Cryptosporidium parvum
Componentsribosomal protein L7A
KeywordsDNA BINDING PROTEIN / CYTOKINE / ribosomal protein / High-mobility like protein / Transcription factor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit / ribosome / nucleolus / RNA binding
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / : / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal protein L7A / Ribonucloprotein
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsDong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Hui, R. ...Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Hui, R. / Bochkarev, A. / Artz, J. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionJul 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 1 chain. ...BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 1 chain. The biological unit of the protein is not known.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribosomal protein L7A


Theoretical massNumber of molelcules
Total (without water)14,4721
Polymers14,4721
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.703, 90.703, 31.275
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsbiological unit unknown

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Components

#1: Protein ribosomal protein L7A


Mass: 14472.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7YYQ3, UniProt: A0A7G2HK80*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.7 Å3/Da / Density % sol: 27.6 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7.5
Details: 1.5 M Sodium Citrate and 0.1M Hepes pH 7.5, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97972 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 1.895→17.9 Å / Num. all: 6861 / Num. obs: 6861 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10.7
Reflection shellResolution: 1.895→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.01 / Num. unique all: 228 / Rsym value: 0.397 / % possible all: 61.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
JDirectordata collection
HKL-2000data scaling
MOLREPphasing
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7K

1e7k


Resolution: 1.895→17.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.955 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27028 499 7.3 %RANDOM
Rwork0.19825 ---
obs0.20335 6358 89.86 %-
all-6358 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.988 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å2-1.15 Å20 Å2
2---2.3 Å20 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 1.895→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 30 900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022881
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.9991195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.69725.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.11315161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.825155
X-RAY DIFFRACTIONr_chiral_restr0.160.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02645
X-RAY DIFFRACTIONr_nbd_refined0.2430.2396
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.28
X-RAY DIFFRACTIONr_mcbond_it1.3461.5595
X-RAY DIFFRACTIONr_mcangle_it2.2162929
X-RAY DIFFRACTIONr_scbond_it3.6533315
X-RAY DIFFRACTIONr_scangle_it6.2474.5266
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 30 -
Rwork0.25 321 -
obs--61.26 %

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