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- PDB-4g6q: The crystal structure of a functionally unknown protein Kfla_6221... -

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Basic information

Entry
Database: PDB / ID: 4g6q
TitleThe crystal structure of a functionally unknown protein Kfla_6221 from Kribbella flavida DSM 17836
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Helix Hairpins - #2180 / Helix-turn-helix domain / ArsR-like helix-turn-helix domain / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Helix Hairpins - #2180 / Helix-turn-helix domain / ArsR-like helix-turn-helix domain / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsTan, K. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein Kfla_6221 from Kribbella flavida DSM 17836, CASP Target
Authors: Tan, K. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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_ref_seq_dif / 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_ref_seq_dif.details / _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 uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7815
Polymers40,4932
Non-polymers2883
Water2,738152
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8776
Polymers40,4932
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9230 Å2
ΔGint-104 kcal/mol
Surface area17250 Å2
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules

B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6854
Polymers40,4932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8080 Å2
ΔGint-47 kcal/mol
Surface area17010 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-42 kcal/mol
Surface area24430 Å2
MethodPISA
4
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,56110
Polymers80,9854
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area20200 Å2
ΔGint-173 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.759, 77.759, 140.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsExperimentally unknown. It is predicted that the chain A and the chain B form dimers with their symmetry-related molecules by the operation ( -y,-x,-z-1/2 ), respectively.

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Components

#1: Protein Putative uncharacterized protein


Mass: 20246.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_6221 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2PVI4
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris:HCl, 1.5M Ammonium Phosphate Dibasic, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.08→40.5 Å / Num. all: 26743 / Num. obs: 26743 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 36.98 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 49.3
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 13 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1305 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→40.158 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1343 5.04 %random
Rwork0.1894 ---
obs0.1918 26657 99.82 %-
all-26657 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.724 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7334 Å20 Å2-0 Å2
2--0.7334 Å20 Å2
3----1.4669 Å2
Refinement stepCycle: LAST / Resolution: 2.08→40.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 15 152 2854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082760
X-RAY DIFFRACTIONf_angle_d1.0353768
X-RAY DIFFRACTIONf_dihedral_angle_d15.3421006
X-RAY DIFFRACTIONf_chiral_restr0.069453
X-RAY DIFFRACTIONf_plane_restr0.005487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0797-2.1540.26531180.21372489260799
2.154-2.24030.29951360.20282465100
2.2403-2.34220.28391240.20512499100
2.3422-2.46570.26451450.21692472100
2.4657-2.62010.2361200.19072512100
2.6201-2.82240.2391490.20842500100
2.8224-3.10630.23381370.20242529100
3.1063-3.55560.24621720.19762509100
3.5556-4.47870.23671310.16632585100
4.4787-40.16550.19931110.1812275499
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)
16.89483.15990.61064.84811.58357.00250.06170.4347-1.1447-0.71030.28960.1306-0.34030.3244-0.22960.2818-0.0713-0.0550.61820.01090.3497-3.2389-17.7655-33.8006
25.4213-1.3625-2.47752.60430.43193.02230.0345-0.4654-0.12460.26370.01940.0945-0.02390.0179-0.08520.19-0.04520.02770.34490.05820.1885-3.2987-18.1927-18.8077
35.4838-0.8397-3.66357.046-1.78134.68270.2385-1.0712-1.39040.8723-0.10810.52181.5715-0.24720.00740.5579-0.16660.02720.55620.19770.549-4.4258-30.1726-16.2992
40.5204-2.16531.97039.5513-9.97681.9970.3078-0.4426-0.385-0.85050.11310.45422.22931.6995-0.29510.51960.1609-0.02771.0919-0.17220.4456-1.6228-24.482-39.9202
57.33571.24352.75573.77522.10346.655-0.1293-0.42710.48580.2627-0.22260.1315-0.2315-0.5120.32140.23390.01120.04690.16850.05530.16036.3668-7.4168-28.2389
61.6723-0.339-0.38471.24830.06042.7478-0.0234-0.1522-0.1554-0.0387-0.02950.00620.04760.00710.0580.17920.00220.02140.18980.01690.165316.6067-19.2274-34.4779
77.2381-1.9753-0.79373.631-0.75376.55240.2752-0.24691.24840.65060.1824-0.1895-0.8797-0.5286-0.39370.6644-0.01310.2220.3042-0.06160.5026-5.17928.0264-19.8142
89.3388-6.66940.98224.7598-0.71220.40110.2851-0.75650.19271.2026-0.20950.56160.0098-0.6627-0.33850.8137-0.06090.29460.664-0.01020.6351-13.9059-1.9486-11.4196
95.89411.24652.03042.08011.03823.89920.4546-1.30550.61061.163-0.333-0.2358-0.44470.4155-0.69920.8644-0.1630.17890.561-0.11180.573-2.87252.6779-9.1822
104.2222-1.9093.10218.5052.0873.87520.4478-1.14431.39680.2933-0.0918-0.5435-1.3446-0.7425-0.42381.37250.02150.56790.6544-0.38430.8686-8.222114.1766-9.8225
115.0047-2.66440.12766.74942.43534.28030.6105-1.72840.33641.97060.1827-0.2124-0.8347-0.2767-0.32112.0052-0.45420.45232.0960.21080.7516-15.06077.71891.6221
123.2954-1.3656-2.76970.57051.15732.34331.3165-0.76832.53331.09210.28941.6868-0.78110.3875-1.64440.9466-0.1510.46090.64-0.10541.4601-5.316515.5883-16.4596
138.93914.86370.51228.1349-1.15552.84560.474-0.89650.11770.3193-0.3164-0.0061-0.4166-0.4645-0.28970.53850.10330.19410.44750.08350.5753-4.01624.4678-29.7646
145.3974-2.84762.25234.5733-2.72876.9120.301-0.1574-0.6583-0.03810.56841.2228-0.2189-1.3068-0.41960.35110.24870.18911.15220.5961.1157-22.9813-5.4675-32.7847
150.62751.19040.38412.4860.10472.35260.0211-0.33190.31940.25090.2730.7145-0.9451-0.8035-0.50440.54040.25480.15470.7130.39711.0688-13.460813.7939-41.5451
161.53360.2105-0.33760.5808-0.04072.752-0.0647-0.06720.6499-0.0792-0.45830.197-0.9433-0.2791-0.79131.14230.5840.66920.7310.20971.2926-15.644524.1672-33.0964
171.65190.25910.92440.86460.85271.12450.59090.0230.19180.5044-0.02271.0595-0.731-1.1161-0.10060.61270.21180.50890.64260.24310.8433-18.28410.9034-28.5469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:19)
2X-RAY DIFFRACTION2chain 'A' and (resseq 20:61)
3X-RAY DIFFRACTION3chain 'A' and (resseq 62:82)
4X-RAY DIFFRACTION4chain 'A' and (resseq 83:95)
5X-RAY DIFFRACTION5chain 'A' and (resseq 96:128)
6X-RAY DIFFRACTION6chain 'A' and (resseq 129:179)
7X-RAY DIFFRACTION7chain 'B' and (resseq 5:35)
8X-RAY DIFFRACTION8chain 'B' and (resseq 36:47)
9X-RAY DIFFRACTION9chain 'B' and (resseq 48:61)
10X-RAY DIFFRACTION10chain 'B' and (resseq 62:68)
11X-RAY DIFFRACTION11chain 'B' and (resseq 69:78)
12X-RAY DIFFRACTION12chain 'B' and (resseq 79:95)
13X-RAY DIFFRACTION13chain 'B' and (resseq 96:119)
14X-RAY DIFFRACTION14chain 'B' and (resseq 120:128)
15X-RAY DIFFRACTION15chain 'B' and (resseq 129:140)
16X-RAY DIFFRACTION16chain 'B' and (resseq 141:159)
17X-RAY DIFFRACTION17chain 'B' and (resseq 160:179)

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