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- PDB-3d0f: Structure of the BIG_1156.2 domain of putative penicillin-binding... -

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Basic information

Entry
Database: PDB / ID: 3d0f
TitleStructure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718
ComponentsPenicillin-binding 1 transmembrane protein MrcA
KeywordsTRANSFERASE / BIG_1156.2 / penicillin-binding 1 / Nitrosomonas europaea / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Cell shape / Cell wall biogenesis/degradation / Glycosyltransferase / Peptidoglycan synthesis / Transmembrane / UNKNOWN FUNCTION
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Nucleic acid-binding proteins / Beta-lactamase/transpeptidase-like ...Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Nucleic acid-binding proteins / Beta-lactamase/transpeptidase-like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsCuff, M.E. / Mulligan, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718.
Authors: Cuff, M.E. / Mulligan, R. / Clancy, S. / Joachimiak, A.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 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: Penicillin-binding 1 transmembrane protein MrcA
B: Penicillin-binding 1 transmembrane protein MrcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5924
Polymers23,4052
Non-polymers1872
Water6,810378
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-21.6 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.206, 52.219, 56.860
Angle α, β, γ (deg.)90.000, 107.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Penicillin-binding 1 transmembrane protein MrcA / Peptidoglycan synthetase


Mass: 11702.283 Da / Num. of mol.: 2 / Fragment: Targeted domain: Residues 318-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Strain: IFO 14298 / Gene: mrcA, NE2317 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21(DE3)
References: UniProt: Q81ZZ3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97959, 0.97970
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979591
20.97971
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 9.8 / Number: 191331 / Rmerge(I) obs: 0.069 / Χ2: 1.53 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 27910 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.955098.710.0463.5187.1
3.133.9599.910.0553.0987.4
2.743.1310010.0662.5117.5
2.492.7410010.0691.7877.5
2.312.4910010.0721.487.5
2.172.3110010.0771.3337.5
2.062.1710010.0871.27.5
1.972.0610010.1051.0637.5
1.91.9710010.1290.957.5
1.831.910010.1680.8957.4
1.771.8310010.2190.8297.3
1.721.7710010.2760.8016.9
1.681.7299.910.3350.7995.9
1.641.6897.210.3470.7934.6
1.61.6486.110.3820.8213.2
ReflectionResolution: 1.6→50 Å / Num. all: 27910 / Num. obs: 27910 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.528 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1823 / Χ2: 0.821 / % possible all: 97.2

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.6 Å / D res low: 50 Å / FOM : 0.28 / FOM acentric: 0.294 / FOM centric: 0 / Reflection: 27886 / Reflection acentric: 26651 / Reflection centric: 1235
Phasing MAD setR cullis acentric: 1.69 / R cullis centric: 1 / Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Loc acentric: 0 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 26651 / Reflection centric: 1235
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
10.46-501.560.10.17424
5.84-10.461.670.10.143162
4.05-5.841.260.10.11074105
3.1-4.051.160.10.12021137
2.51-3.11.570.103258177
2.11-2.511.82004784213
1.82-2.112.21006597248
1.6-1.823.55008412269
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se25.716910.4630.4990.3230
2Se33.96110.8480.5180.7950
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.46-500.3540.4690987424
5.84-10.460.4740.542049343162
4.05-5.840.4630.508011791074105
3.1-4.050.480.513021582021137
2.51-3.10.4730.499034353258177
2.11-2.510.3920.409049974784213
1.82-2.110.2330.241068456597248
1.6-1.820.0920.094086818412269
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 27886
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.13-10062.50.714515
4.87-6.1353.60.898504
4.24-4.8755.70.898520
3.81-4.2455.30.903579
3.49-3.8157.70.884647
3.24-3.4958.50.879685
3.03-3.2455.60.872756
2.86-3.0357.90.881778
2.72-2.8653.30.878821
2.59-2.72560.878872
2.49-2.5957.50.863923
2.39-2.4956.20.879935
2.3-2.3957.40.866996
2.23-2.357.90.8771002
2.16-2.23580.8671060
2.09-2.1658.50.8771079
2.03-2.0963.60.8731118
1.98-2.03650.851153
1.93-1.9864.50.8691174
1.88-1.9365.90.8681208
1.84-1.8869.80.8651228
1.8-1.8469.10.8481243
1.76-1.872.60.8321314
1.73-1.7675.10.8251300
1.7-1.7377.10.811333
1.66-1.780.70.8291355
1.63-1.6683.20.7941335
1.6-1.6385.60.7641453

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.64→35.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.628 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1316 5 %RANDOM
Rwork0.17 ---
all0.173 26155 --
obs0.173 26155 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.66 Å2
2--0.68 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.64→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 11 378 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221768
X-RAY DIFFRACTIONr_bond_other_d0.0020.021290
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9952401
X-RAY DIFFRACTIONr_angle_other_deg0.95233165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21624.07481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35215345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7161518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_nbd_refined0.2210.2319
X-RAY DIFFRACTIONr_nbd_other0.2020.21447
X-RAY DIFFRACTIONr_nbtor_refined0.170.2831
X-RAY DIFFRACTIONr_nbtor_other0.0870.21003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.234
X-RAY DIFFRACTIONr_mcbond_it1.5121.51341
X-RAY DIFFRACTIONr_mcbond_other0.321.5441
X-RAY DIFFRACTIONr_mcangle_it1.78121776
X-RAY DIFFRACTIONr_scbond_it2.7993729
X-RAY DIFFRACTIONr_scangle_it4.0684.5612
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 90 -
Rwork0.215 1797 -
all-1887 -
obs--97.57 %
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)
10.98730.2953-0.90410.2254-0.42391.9759-0.05470.0154-0.0487-0.0609-0.047-0.06750.08130.0480.1018-0.0618-0.0071-0.0007-0.0821-0.0325-0.057811.96022.186320.4034
21.45310.0946-1.6240.0368-0.25313.21370.040.07380.0827-0.05460.0419-0.0009-0.0493-0.2905-0.0818-0.04350.00030.0013-0.0959-0.0222-0.0254-1.32060.843228.1782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA316 - 4202 - 106
2X-RAY DIFFRACTION2BB316 - 4202 - 106

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