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- PDB-2fyw: Crystal Structure of a Conserved Protein of Unknown Function from... -

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Basic information

Entry
Database: PDB / ID: 2fyw
TitleCrystal Structure of a Conserved Protein of Unknown Function from Streptococcus pneumoniae
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / PSI / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / Protein Structure Initiative
Function / homology
Function and homology information


DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / NIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsNocek, B. / Hatzos, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a conserved hypothetical protein from Streptococcus pneumoniae TIGR4
Authors: Nocek, B. / Hatzos, C. / Abdullah, J. / Jaochimiak, A.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S), TWO OF THEM BEING ASSOCIATED INTO DIMER. THE AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THE PROTEIN IS UNKNOWN; HOWEVER THE CRYSTALLOGRAPHIC ANALYSIS INDICATES THAT POLYPEPTIDES ASSOCIATE INTO A HEXAMERIC RING (A TRIMER OF DIMERS).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)90,9553
Polymers90,9553
Non-polymers00
Water3,549197
1
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein

A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)181,9106
Polymers181,9106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area15600 Å2
ΔGint-74 kcal/mol
Surface area64700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.481, 167.016, 122.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 1 - 265 / Label seq-ID: 3 - 267

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
12AA
22BB
32CC

NCS ensembles :
ID
1
2
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN, TWO OF THEM BEING ASSOCIATED INTO DIMER. THE BIOLOGICAL UNIT OF THE PROTEIN IS UNKNOWN, ALTHOUGH THE CRYSTALLOGRAPHIC ANALYSIS INDICATES THAT DIMER IS LIKELY RELEVANT OLIGOMERIC FORM.

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Components

#1: Protein conserved hypothetical protein


Mass: 30318.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: PMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 14973101, UniProt: Q97PK0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 % PEG P400, 0.1 M Na acetate, 0.2 M Calcium acetate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 38726 / Num. obs: 38726 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 17.9
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.107 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.386 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25901 1944 5 %RANDOM
Rwork0.19988 ---
all0.20312 38726 --
obs0.20309 36782 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---1.61 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6331 0 0 197 6528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226505
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9518829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.65525.255314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.915151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7411528
X-RAY DIFFRACTIONr_chiral_restr0.1260.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024953
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22775
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.54156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54626468
X-RAY DIFFRACTIONr_scbond_it2.3732745
X-RAY DIFFRACTIONr_scangle_it3.7894.52361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Number: 2048 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Amedium positional0.280.5
12Bmedium positional0.30.5
13Cmedium positional0.350.5
21Amedium positional0.280.5
22Bmedium positional0.30.5
23Cmedium positional0.350.5
11Amedium thermal0.672
12Bmedium thermal0.632
13Cmedium thermal0.662
21Amedium thermal0.672
22Bmedium thermal0.632
23Cmedium thermal0.662
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 139 -
Rwork0.258 2667 -
obs--99.08 %
Refinement TLS params.Method: refined / Origin x: 18.2826 Å / Origin y: 20.4328 Å / Origin z: 77.1664 Å
111213212223313233
T0.0323 Å20.0051 Å2-0.0177 Å2--0.0009 Å20.0014 Å2--0.0047 Å2
L0.0588 °2-0.0088 °20.0637 °2-0.005 °2-0.0225 °2--0.1148 °2
S-0.0013 Å °-0.0131 Å °-0.0106 Å °0.0109 Å °-0.0016 Å °0.0159 Å °0.016 Å °-0.0184 Å °0.003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2653 - 267
2X-RAY DIFFRACTION1BB1 - 2653 - 267
3X-RAY DIFFRACTION1CC1 - 2653 - 267

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