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- PDB-39pb: Crystal structure of a septum formation protein Maf from Coccidio... -

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Basic information

Entry
Database: PDB / ID: 39pb
TitleCrystal structure of a septum formation protein Maf from Coccidioides immitis (AMP complex)
ComponentsSeptum formation protein Maf
KeywordsCELL CYCLE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / septum formation protein Maf / Coccidioides immitis
Function / homologyNucleoside triphosphate pyrophosphatase Maf-like protein / Maf-like protein / Inosine triphosphate pyrophosphatase-like / nucleoside triphosphate diphosphatase activity / ADENOSINE MONOPHOSPHATE / Septum formation protein Maf
Function and homology information
Biological speciesCoccidioides immitis RS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Crystal structure of a septum formation protein Maf from Coccidioides immitis (AMP complex)
Authors: Ung, A.R. / Lovell, S. / Battaile, K.P.
History
DepositionOct 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septum formation protein Maf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8363
Polymers27,3961
Non-polymers4392
Water45025
1
A: Septum formation protein Maf
hetero molecules

A: Septum formation protein Maf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6716
Polymers54,7932
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4100 Å2
ΔGint-25 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.223, 76.223, 174.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Septum formation protein Maf


Mass: 27396.418 Da / Num. of mol.: 1 / Fragment: P42-L268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis RS (fungus) / Gene: CIMG_03133 / Plasmid: CoimA.00961.a.A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3KAP5
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#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.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.63 Å3/Da / Density % sol: 73.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus Fusion G7: 12.5% (v/v) MPD; 12.5% PEG 1000; 12.5% (w/v) PEG 3350; 0.05M Tris (base); 0.05M BICINE pH 8.5; 0.3% w/v NDSB 195, 0.3% w/v NDSB 201, 0.3% w/v NDSB 211, 0.3% w/v NDSB 221, ...Details: Morpheus Fusion G7: 12.5% (v/v) MPD; 12.5% PEG 1000; 12.5% (w/v) PEG 3350; 0.05M Tris (base); 0.05M BICINE pH 8.5; 0.3% w/v NDSB 195, 0.3% w/v NDSB 201, 0.3% w/v NDSB 211, 0.3% w/v NDSB 221, 0.3% w/v NDSB 256; 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide , CoimA.00961.a.A2.PW39528 at 13.2 mg/mL. cocrystallization with 25 mM AMP disodium salt and 20 mM Magnesium chloride hexahydrate. plate 21398 G7 drop 1, Puck: PSL-0109, Cryo: direct.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 26, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.33→46.3 Å / Num. obs: 22907 / % possible obs: 100 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.018 / Rrim(I) all: 0.088 / Χ2: 1 / Net I/σ(I): 24.4 / Num. measured all: 587279
Reflection shellResolution: 2.33→2.41 Å / % possible obs: 99.9 % / Redundancy: 25.1 % / Rmerge(I) obs: 1.987 / Num. measured all: 55108 / Num. unique obs: 2195 / CC1/2: 0.904 / Rpim(I) all: 0.402 / Rrim(I) all: 2.028 / Χ2: 0.96 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(2.2.1_6174: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→46.3 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1085 4.76 %
Rwork0.2091 --
obs0.2113 22776 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 29 25 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041776
X-RAY DIFFRACTIONf_angle_d0.7282421
X-RAY DIFFRACTIONf_dihedral_angle_d17.703671
X-RAY DIFFRACTIONf_chiral_restr0.044293
X-RAY DIFFRACTIONf_plane_restr0.007308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.440.43471420.3542631X-RAY DIFFRACTION99
2.44-2.560.26231200.28372664X-RAY DIFFRACTION100
2.56-2.730.2871390.24682646X-RAY DIFFRACTION100
2.73-2.940.31991490.27482659X-RAY DIFFRACTION99
2.94-3.230.32261390.26362665X-RAY DIFFRACTION100
3.23-3.70.26871310.22622729X-RAY DIFFRACTION100
3.7-4.660.23371130.17732779X-RAY DIFFRACTION100
4.66-46.30.22131520.17842918X-RAY DIFFRACTION100
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)
18.7974-0.83292.30543.91770.32233.2137-0.2103-0.61430.64150.19940.17710.0303-0.33790.27470.17050.5308-0.0646-0.0440.621-0.01360.6293-0.6574-18.715712.664
23.6901-0.12311.46362.6732-1.22321.2637-0.00631.0094-0.5415-0.87270.44850.07550.12391.1040.01290.87070.0311-0.02810.8173-0.08540.73923.4125-31.711.0091
31.2291-0.2821.99890.1843-0.2473.5470.17470.0704-0.0385-0.1287-0.1109-0.14030.31320.4598-0.1060.5932-0.0251-0.05480.4938-0.06480.55-5.6959-27.6519-6.3148
41.9982-0.5239-0.68110.69920.71650.85710.1708-0.2027-0.3746-0.02960.24160.19260.0514-0.462900.7262-0.1173-0.10850.4272-0.04810.6204-10.8992-26.1841-4.5782
50.0597-0.06090.02680.0616-0.02830.0230.2513-0.03680.48110.44960.0194-0.4609-1.15690.1643-0.00020.8513-0.1365-0.00860.7963-0.11080.7617-9.3831-16.6134-12.3101
60.163-0.1561-0.20220.42120.07580.2958-0.2288-0.53880.0260.12180.2203-0.2396-0.2035-0.3586-0.00070.7066-0.0973-0.04870.5926-0.03180.607-16.5263-19.9294-3.6694
71.44210.24531.77274.8794-1.98363.2552-0.2683-0.61150.1710.19260.15020.6889-0.2807-0.3176-0.13320.6466-0.0969-0.01780.66910.0180.5784-5.1005-30.45815.8748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 227 )
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 264 )

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