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- PDB-3p42: Structure of GfcC (YmcB), protein encoded by the E. coli group 4 ... -

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Basic information

Entry
Database: PDB / ID: 3p42
TitleStructure of GfcC (YmcB), protein encoded by the E. coli group 4 capsule operon
ComponentsPredicted protein
KeywordsUNKNOWN FUNCTION / Beta-Grasp
Function / homology
Function and homology information


Ubiquitin-like (UB roll) - #700 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Capsule biosynthesis GfcC-like, C-terminal / Capsule biosynthesis GfcC-like, N-terminal / Capsule biosynthesis GfcC C-terminal / Capsule biosynthesis GfcC, N-terminal / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Ubiquitin-like (UB roll) - #700 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Capsule biosynthesis GfcC-like, C-terminal / Capsule biosynthesis GfcC-like, N-terminal / Capsule biosynthesis GfcC C-terminal / Capsule biosynthesis GfcC, N-terminal / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsSaper, M.A. / Sathiyamoorthy, K.
CitationJournal: Biochemistry / Year: 2011
Title: The Crystal Structure of Escherichia coli Group 4 Capsule Protein GfcC Reveals a Domain Organization Resembling That of Wza.
Authors: Sathiyamoorthy, K. / Mills, E. / Franzmann, T.M. / Rosenshine, I. / Saper, M.A.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
A: Predicted protein
B: Predicted protein
C: Predicted protein
D: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3537
Polymers105,0644
Non-polymers2883
Water12,484693
1
A: Predicted protein


Theoretical massNumber of molelcules
Total (without water)26,2661
Polymers26,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4583
Polymers26,2661
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Predicted protein


Theoretical massNumber of molelcules
Total (without water)26,2661
Polymers26,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3622
Polymers26,2661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Predicted protein
B: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7244
Polymers52,5322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-25 kcal/mol
Surface area22010 Å2
MethodPISA
6
C: Predicted protein
D: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6283
Polymers52,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-16 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.831, 99.980, 69.020
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and resi 31:35B0
211chain D and resi 31:35D0

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Components

#1: Protein
Predicted protein


Mass: 26266.117 Da / Num. of mol.: 4 / Fragment: UNP residues 22-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Strain: E2348/69 / Gene: E2348C_0970, E2348_C_0970, gfcC / Plasmid: pETBlue2 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) pLacI / References: UniProt: B7UN63
#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.: 693 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5 M Ammonium Sulfate, 0.1 M NaCl, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2010
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.77→49 Å / Num. obs: 81677 / Redundancy: 6.8 % / Biso Wilson estimate: 25.01 Å2

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Processing

Software
NameVersionClassification
MAR345data collection
PHASER(in PHENIX)phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.91→34.494 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8582 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.93 / Stereochemistry target values: ML
Details: Refinement was with anomalous data, F+ and F- were refined as separate reflections.
RfactorNum. reflection% reflection
Rfree0.2168 7024 5 %
Rwork0.1729 133477 -
obs0.1752 140501 98.46 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.964 Å2 / ksol: 0.433 e/Å3
Displacement parametersBiso max: 242.89 Å2 / Biso mean: 40.8623 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.9226 Å20 Å20.4583 Å2
2--1.7601 Å2-0 Å2
3---0.1625 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 15 693 7788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087303
X-RAY DIFFRACTIONf_angle_d1.1110026
X-RAY DIFFRACTIONf_dihedral_angle_d13.4442674
X-RAY DIFFRACTIONf_chiral_restr0.0681161
X-RAY DIFFRACTIONf_plane_restr0.0051310
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B70X-RAY DIFFRACTIONPOSITIONAL0.276
12D70X-RAY DIFFRACTIONPOSITIONAL0.276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.97830.31386610.2623125771323892
1.9783-2.05750.26516730.2045132371391098
2.0575-2.15110.22737260.1812134211414799
2.1511-2.26450.27026650.1943134071407299
2.2645-2.40630.24247340.1742133441407899
2.4063-2.5920.21897200.1665134761419699
2.592-2.85280.21767080.1732135031421199
2.8528-3.26530.21827280.16481352314251100
3.2653-4.11290.19847270.15971348314210100
4.1129-34.49970.18726820.1643135061418899
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)
10.3202-0.0493-0.07430.2678-0.00991.338-0.0008-0.0040.025-0.0240.0701-0.0167-0.12-0.029-0.06090.15470.00160.01380.1028-0.00970.15648.6934-0.33955.2368
20.4681-0.14910.48480.4013-0.10331.32680.10580.0654-0.00420.0572-0.02530.00260.10.2716-0.07670.16130.0092-0.00230.2012-0.02820.153326.5499-6.844-22.7699
30.7928-0.0189-0.08330.4094-0.24030.69240.0089-0.00020.042-0.01630.0141-0.01060.00660.0464-0.01720.11480.01650.00470.1104-0.00440.143-4.882524.18027.9281
42.7119-0.3569-0.35930.392-0.21130.2314-0.1233-0.5161-0.24920.05420.05030.0771-0.00980.08260.07280.08640.02240.0010.21250.03740.187123.225217.737324.6702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 23:256)A23 - 256
2X-RAY DIFFRACTION2(chain B and resid 22:246)B22 - 246
3X-RAY DIFFRACTION3(chain C and resid 23:248)C23 - 248
4X-RAY DIFFRACTION4(chain D and resid 23:251)D23 - 251

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