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- PDB-3m05: The crystal structure of a functionally unknown protein PEPE_1480... -

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Basic information

Entry
Database: PDB / ID: 3m05
TitleThe crystal structure of a functionally unknown protein PEPE_1480 from Pediococcus pentosaceus ATCC 25745
Componentsuncharacterized protein PEPE_1480
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyCyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Protein from nitrogen regulatory protein P-II (GLNB) family
Function and homology information
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.145 Å
AuthorsTan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein PEPE_1480 from Pediococcus pentosaceus ATCC 25745
Authors: Tan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Data collection
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_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_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: uncharacterized protein PEPE_1480
B: uncharacterized protein PEPE_1480
C: uncharacterized protein PEPE_1480
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1089
Polymers38,5313
Non-polymers5766
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-104 kcal/mol
Surface area15830 Å2
MethodPISA
2
A: uncharacterized protein PEPE_1480
hetero molecules

A: uncharacterized protein PEPE_1480
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0726
Polymers25,6882
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1720 Å2
ΔGint-43 kcal/mol
Surface area13300 Å2
MethodPISA
3
B: uncharacterized protein PEPE_1480
hetero molecules

C: uncharacterized protein PEPE_1480
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0726
Polymers25,6882
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-y+3/2,x+1/2,z-1/41
Buried area1860 Å2
ΔGint-43 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.774, 119.774, 119.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsExperimentally unknown. The chains A, B and C may form a trimer.

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Components

#1: Protein uncharacterized protein PEPE_1480


Mass: 12843.794 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Strain: ATCC 25745 / Gene: PEPE_1480 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q03E61
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 5.55 Å3/Da / Density % sol: 77.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Li2SO4, 0.1M MES, 20% (v/v)1,4-butanodiol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937, 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979511
ReflectionResolution: 3.145→37.862 Å / Num. all: 15624 / Num. obs: 15624 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 27.2
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.4 / Num. unique all: 749 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.145→37.862 Å / SU ML: 0.26 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 739 5 %random
Rwork0.196 ---
all0.1985 14772 --
obs0.1985 14772 94.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.084 Å2 / ksol: 0.293 e/Å3
Refinement stepCycle: LAST / Resolution: 3.145→37.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 30 5 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012371
X-RAY DIFFRACTIONf_angle_d1.2953207
X-RAY DIFFRACTIONf_dihedral_angle_d21.087873
X-RAY DIFFRACTIONf_chiral_restr0.076382
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1448-3.38750.36021350.28172465X-RAY DIFFRACTION85
3.3875-3.72810.25281360.21822702X-RAY DIFFRACTION93
3.7281-4.26690.19381420.16472864X-RAY DIFFRACTION97
4.2669-5.37340.16171700.11942920X-RAY DIFFRACTION99
5.3734-37.86510.30781560.23013082X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.3778-0.69160.18371.4865-1.26171.2716-0.1943-0.3578-0.32150.26640.23330.3164-0.1603-0.2704-0.07370.6539-0.0778-0.02210.76170.07540.663261.8378110.361153.8182
21.10440.6718-1.53880.9752-0.91052.1746-0.1743-0.1806-0.0043-0.2136-0.1127-0.37710.34530.37630.25480.6070.02340.06670.7069-0.11490.7797
31.4994-1.1244-0.90180.91390.6310.94640.23120.27960.2988-0.3054-0.0547-0.2116-0.2831-0.1925-0.12570.7950.0887-0.10720.5785-0.00240.6949
Refinement TLS groupSelection details: chain C

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