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- PDB-3qtd: Crystal structure of putative modulator of gyrase (PmbA) from Pse... -

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Basic information

Entry
Database: PDB / ID: 3qtd
TitleCrystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1
ComponentsPmbA protein
KeywordsGENE REGULATION / putative modulator of gyrase (PmbA) / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


metallopeptidase activity / cytosol
Similarity search - Function
PmbA/TldD fold / PmbA/TldD superfamily / PmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase central domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsTkaczuk, K.L. / Chruszcz, M. / Evdokimova, E. / Liu, F. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1
Authors: Tkaczuk, K.L. / Chruszcz, M. / Evdokimova, E. / Liu, F. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PmbA protein
B: PmbA protein
C: PmbA protein
D: PmbA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,17613
Polymers193,3474
Non-polymers8299
Water6,395355
1
A: PmbA protein
hetero molecules

D: PmbA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1347
Polymers96,6742
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y+1/2,-z+3/21
Buried area3890 Å2
ΔGint-11 kcal/mol
Surface area35380 Å2
MethodPISA
2
B: PmbA protein
C: PmbA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0426
Polymers96,6742
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-11 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.385, 116.201, 253.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A9 - 448
2113B9 - 448
3113C9 - 448
4113D9 - 448

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Components

#1: Protein
PmbA protein / Putative modulator of gyrase


Mass: 48336.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4472, pmbA, PmbA_TldD / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9HVU9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Mg Formate, 20% P3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 56209 / Num. obs: 56209 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.171 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2777 / Rsym value: 0.731 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000SHELXDphasing
SHELXEmodel building
DMmodel building
MLPHAREphasing
RESOLVEmodel building
CCP4model building
REFMAC5.6.0070refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 30.517 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27863 2830 5.1 %RANDOM
Rwork0.22461 ---
all0.22742 53114 --
obs0.22742 53114 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.182 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å20 Å2
2--5.08 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13195 0 54 355 13604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02113464
X-RAY DIFFRACTIONr_bond_other_d00.029067
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.95618217
X-RAY DIFFRACTIONr_angle_other_deg4.335321883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16251762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41622.997614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98152107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.26615135
X-RAY DIFFRACTIONr_chiral_restr0.1210.22022
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215509
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022882
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2577tight positional0.110.05
B2577tight positional0.130.05
C2577tight positional0.110.05
D2577tight positional0.110.05
A2927loose positional0.325
B2927loose positional0.285
C2927loose positional0.35
D2927loose positional0.225
A2577tight thermal3.810.5
B2577tight thermal3.720.5
C2577tight thermal3.460.5
D2577tight thermal3.820.5
A2927loose thermal5.6110
B2927loose thermal5.9210
C2927loose thermal5.6410
D2927loose thermal5.8810
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 211 -
Rwork0.331 3706 -
obs--93.8 %
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)
10.32070.0876-0.09050.4329-0.02750.7565-0.01370.0772-0.03360.05280.00440.0534-0.01660.14170.00940.0661-0.00440.01370.0564-0.01150.027743.53346.532159.042
20.30570.12350.35550.37550.07610.4286-0.0047-0.05320.0044-0.0213-0.0088-0.0644-0.0087-0.06690.01350.0929-0.0083-0.00060.0220.01870.054325.86211.76146.84
30.28760.1429-0.40930.3595-0.0860.86850.0311-0.0063-0.02030.0054-0.02540.03820.07160.0122-0.00560.1313-0.0091-0.00790.0450.03440.08437.41-10.369160.864
40.7174-0.22220.44130.4564-0.24721.2077-0.0060.09280.03840.0198-0.02580.0234-0.1352-0.02260.03170.1147-0.0024-0.00480.03570.02050.056437.3710.688207.889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 448
2X-RAY DIFFRACTION2B8 - 448
3X-RAY DIFFRACTION3C8 - 448
4X-RAY DIFFRACTION4D8 - 448

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