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- PDB-3fdx: Putative filament protein / universal stress protein F from Klebs... -

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Basic information

Entry
Database: PDB / ID: 3fdx
TitlePutative filament protein / universal stress protein F from Klebsiella pneumoniae.
ComponentsPutative filament protein / universal stress protein F
Keywordsstructural genomics / unknown function / APC60640.1 / filament protein / universal stress protein F / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FORMIC ACID / Universal stress protein F
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsOsipiuk, J. / Volkart, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative filament protein / universal stress protein F from Klebsiella pneumoniae.
Authors: Osipiuk, J. / Volkart, L. / Bearden, J. / Joachimiak, A.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Putative filament protein / universal stress protein F
B: Putative filament protein / universal stress protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9499
Polymers31,7692
Non-polymers1,1797
Water4,828268
1
A: Putative filament protein / universal stress protein F
hetero molecules

A: Putative filament protein / universal stress protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9248
Polymers31,7692
Non-polymers1,1556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4150 Å2
ΔGint-30 kcal/mol
Surface area12000 Å2
MethodPISA
2
B: Putative filament protein / universal stress protein F
hetero molecules

B: Putative filament protein / universal stress protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,97310
Polymers31,7692
Non-polymers1,2048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4180 Å2
ΔGint-37 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.684, 67.684, 161.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsputative biological unit is a dimer formed by one of monomers and its neighbor generated by crystallographic symmetry (based on PISA)

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Components

#1: Protein Putative filament protein / universal stress protein F


Mass: 15884.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_14150, KPN_01444, ynaF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6T8F5
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3 M magnesium formate, 0.1 M Bis-Tris buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 8, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.58→33.7 Å / Num. all: 58049 / Num. obs: 58049 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.05 / Χ2: 2.437 / Net I/σ(I): 58.999
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.92 / Num. unique all: 2290 / Χ2: 0.906 / % possible all: 77.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→33.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.242 / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.878 / SU B: 2.621 / SU ML: 0.046 / SU R Cruickshank DPI: 0.091 / SU Rfree: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2942 5.1 %RANDOM
Rwork0.187 ---
all0.188 57977 --
obs0.188 57977 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.62 Å2 / Biso mean: 20.275 Å2 / Biso min: 2.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.58→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 71 268 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222291
X-RAY DIFFRACTIONr_bond_other_d0.0010.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.9452.0153164
X-RAY DIFFRACTIONr_angle_other_deg1.04333815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67324.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04815417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9861517
X-RAY DIFFRACTIONr_chiral_restr0.1040.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02424
X-RAY DIFFRACTIONr_mcbond_it1.1821.51396
X-RAY DIFFRACTIONr_mcbond_other0.3321.5542
X-RAY DIFFRACTIONr_mcangle_it2.03122309
X-RAY DIFFRACTIONr_scbond_it2.7173895
X-RAY DIFFRACTIONr_scangle_it4.5014.5829
LS refinement shellResolution: 1.579→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 179 -
Rwork0.347 3227 -
all-3406 -
obs-3406 78.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.6532.0602-1.52053.01211.3493.26450.031-0.0554-0.13980.052-0.0933-0.07490.0225-0.05130.06240.09330.062-0.02620.0662-0.02720.066655.83512.94115.037
28.1753-3.61011.33211.6031-0.57820.23540.11780.71411.1611-0.1425-0.3069-0.5224-0.06270.1860.18910.8535-0.07720.01930.48650.07860.511863.93223.88.686
34.90720.59561.85121.38241.74482.97620.068-0.1078-0.19880.1090.057-0.14180.2601-0.0029-0.12510.10320.0504-0.02610.0564-0.03720.049962.7029.42618.212
41.34961.1820.86772.50540.10876.6584-0.14940.25510.1431-0.2875-0.06090.2544-0.2309-0.2540.21030.16230.049-0.0360.1597-0.01440.031953.65215.4460.513
50.0830.25640.15981.1894-0.14041.3741-0.024-0.0087-0.0101-0.1365-0.0747-0.0768-0.02240.00260.09880.0990.0822-0.04050.0705-0.03890.048456.27710.66510.129
60.2079-0.4593-0.20981.50.18230.56090.0570.065-0.037-0.0191-0.04220.0283-0.1188-0.115-0.01470.09140.0673-0.01980.0559-0.02540.049153.14220.78519.873
71.5045-0.25690.0422.5198-0.55454.32810.104-0.09470.25210.2972-0.15670.30130.2843-0.15960.05280.12260.01350.0870.1011-0.02560.09941.70645.1513.739
84.789-0.284-3.638312.38052.47383.1827-0.1074-0.0468-0.0602-0.14170.1512-0.24770.06930.0672-0.04370.2050.0199-0.05420.13610.0030.279331.25637.92514.382
91.3551-0.07640.15211.847-0.46791.69050.02050.0860.11580.03880.00440.0986-0.1295-0.0527-0.02490.05610.0420.02910.03710.03130.043138.82650.27416.083
105.76361.2807-4.50520.3793-0.3198.5174-0.17510.3025-0.1175-0.00440.1092-0.03430.33360.02130.0660.06540.0336-0.00740.09030.03080.054141.00445.252-0.301
110.2852-0.43050.47061.83050.23821.59420.0110.09840.0554-0.2189-0.22560.1211-0.19840.03740.21450.09020.08030.0080.11120.05240.076339.39552.4059.271
120.2124-0.32410.10780.5289-0.14620.72920.04290.03190.0267-0.0232-0.0173-0.0090.11610.0901-0.02570.08160.0540.02290.03830.02260.047546.43639.59619.05
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 8
2X-RAY DIFFRACTION2A9 - 14
3X-RAY DIFFRACTION3A15 - 35
4X-RAY DIFFRACTION4A36 - 73
5X-RAY DIFFRACTION5A74 - 94
6X-RAY DIFFRACTION6A95 - 141
7X-RAY DIFFRACTION7B-1 - 10
8X-RAY DIFFRACTION8B11 - 16
9X-RAY DIFFRACTION9B17 - 40
10X-RAY DIFFRACTION10B57 - 74
11X-RAY DIFFRACTION11B75 - 90
12X-RAY DIFFRACTION12B91 - 141

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