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- PDB-2imh: Crystal structure of protein SPO2555 from Silicibacter pomeroyi, ... -

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Basic information

Entry
Database: PDB / ID: 2imh
TitleCrystal structure of protein SPO2555 from Silicibacter pomeroyi, Pfam DUF1028
ComponentsHypothetical protein UNP Q5LQD5_SILPO
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyProtein of unknown function DUF1028 / Family of unknown function (DUF1028) / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Slocombe, A. / Ozyurt, S. / Wasserman, S. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein from Silicibacter pomeroyi
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Slocombe, A. / Ozyurt, S. / Wasserman, S. / Burley, S.K. / Almo, S.C.
History
DepositionOct 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE MSE -1 is a modified residue and an initiating methionine

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein UNP Q5LQD5_SILPO
B: Hypothetical protein UNP Q5LQD5_SILPO


Theoretical massNumber of molelcules
Total (without water)49,3712
Polymers49,3712
Non-polymers00
Water9,908550
1
A: Hypothetical protein UNP Q5LQD5_SILPO


Theoretical massNumber of molelcules
Total (without water)24,6851
Polymers24,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein UNP Q5LQD5_SILPO


Theoretical massNumber of molelcules
Total (without water)24,6851
Polymers24,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-25 kcal/mol
Surface area17120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.250, 69.594, 105.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsprobable monomer

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Components

#1: Protein Hypothetical protein UNP Q5LQD5_SILPO


Mass: 24685.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO2555 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LQD5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 560mM tri-Sodium Citrate dihydrate, pH 7, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. all: 62233 / Num. obs: 51467 / % possible obs: 82.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 15.4
Reflection shellResolution: 1.57→1.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8896 / Rsym value: 0.044 / % possible all: 27.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.656 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 2615 5.1 %RANDOM
Rwork0.17076 ---
obs0.17253 48829 82.61 %-
all-59107 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.95 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 550 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213426
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9454678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2575467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11724.248153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28915520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg151521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022673
X-RAY DIFFRACTIONr_nbd_refined0.2010.21743
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2431
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.236
X-RAY DIFFRACTIONr_mcbond_it0.9431.52297
X-RAY DIFFRACTIONr_mcangle_it1.13423540
X-RAY DIFFRACTIONr_scbond_it2.23631262
X-RAY DIFFRACTIONr_scangle_it3.2524.51125
LS refinement shellResolution: 1.574→1.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 44 -
Rwork0.258 758 -
obs-758 17.73 %

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