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- PDB-3lae: The crystal structure of a functionally unknown conserved protein... -

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Basic information

Entry
Database: PDB / ID: 3lae
TitleThe crystal structure of a functionally unknown conserved protein from Haemophilus influenzae Rd KW20
Components
  • UPF0053 protein HI0107
  • Unknown peptide fragment
KeywordsMEMBRANE PROTEIN / APC85784.2 / conserved protein / Haemophilus influenzae Rd KW20 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / CBS domain / Cell membrane / Membrane / Transmembrane
Function / homology
Function and homology information


flavin adenine dinucleotide binding / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain / CBS domain / CBS domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / UPF0053 protein HI_0107
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.453 Å
AuthorsTan, K. / Li, H. / Bargassa, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown conserved protein from Haemophilus influenzae Rd KW20
Authors: Tan, K. / Li, H. / Bargassa, M. / Clancy, S. / Joachimiak, A.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJan 19, 2010ID: 2O1R
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0053 protein HI0107
X: Unknown peptide fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7816
Polymers9,5002
Non-polymers2814
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area5360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.604, 77.563, 79.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-143-

HOH

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Components

#1: Protein UPF0053 protein HI0107


Mass: 9164.869 Da / Num. of mol.: 1 / Fragment: sequence database residues 343-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: HI0107 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57017
#2: Protein/peptide Unknown peptide fragment


Mass: 335.399 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide fragment of unknown source, its sequence has been assigned according to electron density
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.4M NaH2PO4, 1.6M K2HPO4, 0.1M Imidazole, 0.2M NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2006 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.45→28 Å / Num. all: 14271 / Num. obs: 14271 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 16.03 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 38.7
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 1.9 / Num. unique all: 664 / % possible all: 94.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.453→27.692 Å / SU ML: 0.18 / σ(F): 0.12 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 680 4.95 %random
Rwork0.1641 ---
obs0.1667 13739 95.77 %-
all-13739 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.026 Å2 / ksol: 0.433 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0894 Å20 Å2-0 Å2
2--1.5595 Å20 Å2
3----1.649 Å2
Refinement stepCycle: LAST / Resolution: 1.453→27.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 0 17 71 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007795
X-RAY DIFFRACTIONf_angle_d1.0521096
X-RAY DIFFRACTIONf_dihedral_angle_d16.998324
X-RAY DIFFRACTIONf_chiral_restr0.07135
X-RAY DIFFRACTIONf_plane_restr0.003142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.453-1.56520.24491310.16262302X-RAY DIFFRACTION87
1.5652-1.72270.22111290.14732571X-RAY DIFFRACTION95
1.7227-1.97190.21071300.12592651X-RAY DIFFRACTION98
1.9719-2.48410.18171530.13182690X-RAY DIFFRACTION99
2.4841-27.69660.23481370.18292845X-RAY DIFFRACTION99

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