- PDB-3fm2: CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) F... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3fm2
Title
CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.80 A RESOLUTION
Components
Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family
Keywords
HEME-BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Intracellular heme transport protein HutX-like / Haem utilisation ChuX/HutX / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / ACETATE ION / Uncharacterized protein
Function and homology information
Biological species
Anabaena variabilis ATCC 29413 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
Journal: To be published Title: Crystal structure of uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family (YP_324846.1) from Anabaena variabilis ATCC 29413 at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG)
A: Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family B: Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family hetero molecules
CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION. ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.
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Components
#1: Protein
Uncharacterizedprotein, distantlyrelatedtoahemebinding/degradingHemS (PF05171) family
Mass: 15564.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria) Gene: Ava_4353, YP_324846.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M4Y5
Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NANODROP, 0.2M Ca(OAc)2, 40.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91162
1
2
0.9787
1
3
0.97828
1
Reflection
Resolution: 1.8→29.001 Å / Num. obs: 25482 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 25.168 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.16
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.8-1.86
0.432
2.03
8422
4421
1
98.8
1.86-1.94
0.29
2.9
9837
5148
1
99.2
1.94-2.03
0.208
3.8
9196
4810
1
99
2.03-2.13
0.141
5.6
8626
4489
1
98.9
2.13-2.27
0.103
7.4
9596
4988
1
99
2.27-2.44
0.081
9.1
9004
4665
1
99.1
2.44-2.69
0.057
12.2
9385
4837
1
99
2.69-3.07
0.038
16.4
9041
4672
1
98.9
3.07-3.87
0.026
23.5
9312
4783
1
98.6
3.87-29.001
0.022
28.9
9226
4709
1
96.9
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.001 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.696 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.123 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ACETATE (ACT) FROM THE CRYSTALLIZATION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ZINC (ZN) HAS BEEN MODELED IN BOTH PROTEIN MOLECULES BASED ON A FLUORESCENCE SCAN AND ANOMALOUS DIFFERENCE FOURIER MAPS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.219
1302
5.1 %
RANDOM
Rwork
0.196
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obs
0.197
25437
99.49 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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