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- PDB-3fm2: CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) F... -

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Basic information

Entry
Database: PDB / ID: 3fm2
TitleCRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.80 A RESOLUTION
ComponentsUncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family
KeywordsHEME-BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


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 / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Heme utilization protein HuvX
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: 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)
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)31,4367
Polymers31,1282
Non-polymers3085
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-10.3 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.230, 61.750, 84.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL 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 Uncharacterized protein, distantly related to a heme binding/degrading HemS (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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS 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

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97870, 0.97828
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97871
30.978281
ReflectionResolution: 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) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.4322.0384224421198.8
1.86-1.940.292.998375148199.2
1.94-2.030.2083.891964810199
2.03-2.130.1415.686264489198.9
2.13-2.270.1037.495964988199
2.27-2.440.0819.190044665199.1
2.44-2.690.05712.293854837199
2.69-3.070.03816.490414672198.9
3.07-3.870.02623.593124783198.6
3.87-29.0010.02228.992264709196.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1302 5.1 %RANDOM
Rwork0.196 ---
obs0.197 25437 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.15 Å2 / Biso mean: 29.96 Å2 / Biso min: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---1.13 Å20 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 14 172 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222147
X-RAY DIFFRACTIONr_bond_other_d0.0010.021421
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9572901
X-RAY DIFFRACTIONr_angle_other_deg0.76733468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5015264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.06924.34892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.86315356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.029156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
X-RAY DIFFRACTIONr_nbd_refined0.1930.2348
X-RAY DIFFRACTIONr_nbd_other0.1810.21411
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21008
X-RAY DIFFRACTIONr_nbtor_other0.0850.21120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2147
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3560.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.220
X-RAY DIFFRACTIONr_symmetry_hbond_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.03121416
X-RAY DIFFRACTIONr_mcbond_other0.1652543
X-RAY DIFFRACTIONr_mcangle_it1.49732105
X-RAY DIFFRACTIONr_scbond_it0.9452918
X-RAY DIFFRACTIONr_scangle_it1.2633796
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 109 -
Rwork0.246 1716 -
all-1825 -
obs--99.02 %
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)
11.114-0.143-0.0551.96560.33521.3922-0.013-0.01440.23010.05130.009-0.14060.01890.02180.004-0.0643-0.0076-0.0056-0.07180.0067-0.030727.05074.705914.0924
22.07160.5845-0.0083.3929-0.8741.6149-0.0295-0.01360.0491-0.16160.08480.38520.0664-0.1048-0.0553-0.0673-0.0028-0.0319-0.03590.0074-0.06044.4121-3.13664.8942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 134
2X-RAY DIFFRACTION2B2 - 134

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