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- PDB-3cqy: Crystal structure of a functionally unknown protein (SO_1313) fro... -

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Basic information

Entry
Database: PDB / ID: 3cqy
TitleCrystal structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1
ComponentsAnhydro-N-acetylmuramic acid kinase
KeywordsTRANSFERASE / APC7501 / SO_1313 / structural genomics / PSI-2 / Shewanella oneidensis MR-1 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Carbohydrate metabolism / Kinase / Nucleotide-binding
Function / homology
Function and homology information


anhydro-N-acetylmuramic acid kinase / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / ATP binding
Similarity search - Function
Anhydro-N-acetylmuramic acid kinase / Anhydro-N-acetylmuramic acid kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Anhydro-N-acetylmuramic acid kinase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsTan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1.
Authors: Tan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 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: Anhydro-N-acetylmuramic acid kinase
B: Anhydro-N-acetylmuramic acid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,82010
Polymers80,3712
Non-polymers4498
Water8,107450
1
A: Anhydro-N-acetylmuramic acid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5286
Polymers40,1861
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anhydro-N-acetylmuramic acid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2924
Polymers40,1861
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Anhydro-N-acetylmuramic acid kinase
B: Anhydro-N-acetylmuramic acid kinase
hetero molecules

A: Anhydro-N-acetylmuramic acid kinase
B: Anhydro-N-acetylmuramic acid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,64120
Polymers160,7434
Non-polymers89816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9570 Å2
ΔGint-32.7 kcal/mol
Surface area54000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.816, 147.816, 117.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. BASED ON THE CRYSTAL STRUCTURE, IT IS LIKELY MONOMERIC

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Components

#1: Protein Anhydro-N-acetylmuramic acid kinase / AnhMurNAc kinase


Mass: 40185.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: NP_716933, anmK, SO_1313 / Plasmid: p15Tv Lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8EHB5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3.5M Na formate, 0.1M Tris-HCl, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2007 / Details: Mirrors
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: 2.3→47.78 Å / Num. all: 58423 / Num. obs: 58423 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 29.7
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3809 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.015 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.18 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21123 2943 5.1 %RANDOM
Rwork0.17269 ---
all0.17462 55302 --
obs0.17462 55302 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.465 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 22 450 6088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9687802
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57924.94249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02515953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4681529
X-RAY DIFFRACTIONr_chiral_restr0.0950.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024365
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.22651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23947
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2414
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.53761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22125833
X-RAY DIFFRACTIONr_scbond_it2.0532249
X-RAY DIFFRACTIONr_scangle_it3.2894.51968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 235 -
Rwork0.236 3955 -
obs-4190 98.7 %
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)
10.4940.8054-0.7381.8745-0.73681.48970.1254-0.0629-0.03990.1987-0.1441-0.03320.0538-0.04960.0187-0.1222-0.0074-0.0193-0.12330.0761-0.098235.103871.955647.1732
20.7303-0.43390.78831.3126-0.50861.51990.06660.1481-0.2283-0.1941-0.03260.10140.138-0.0405-0.034-0.1160.00760.0291-0.08930.0078-0.099734.255182.88838.4288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 3691 - 370
2X-RAY DIFFRACTION2BB1 - 3692 - 370

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