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- PDB-4nkp: Crystal structure of a putative extracellular heme-binding protei... -

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Basic information

Entry
Database: PDB / ID: 4nkp
TitleCrystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution
Componentsputative extracellular heme-binding protein
KeywordsCHAPERONE / PF03928 family protein / DUF336 / putative chaperone / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology: / Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GlcG protein
Function and homology information
Biological speciesDesulfovibrio piger (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.24 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Nov 6, 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: putative extracellular heme-binding protein
B: putative extracellular heme-binding protein
C: putative extracellular heme-binding protein
D: putative extracellular heme-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,89414
Polymers62,9614
Non-polymers93310
Water10,070559
1
A: putative extracellular heme-binding protein
B: putative extracellular heme-binding protein
hetero molecules

A: putative extracellular heme-binding protein
B: putative extracellular heme-binding protein
hetero molecules

A: putative extracellular heme-binding protein
B: putative extracellular heme-binding protein
hetero molecules

A: putative extracellular heme-binding protein
B: putative extracellular heme-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,78128
Polymers125,9238
Non-polymers1,85820
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30450 Å2
ΔGint-204 kcal/mol
Surface area34430 Å2
MethodPISA
2
C: putative extracellular heme-binding protein
D: putative extracellular heme-binding protein
hetero molecules

C: putative extracellular heme-binding protein
D: putative extracellular heme-binding protein
hetero molecules

C: putative extracellular heme-binding protein
D: putative extracellular heme-binding protein
hetero molecules

C: putative extracellular heme-binding protein
D: putative extracellular heme-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,79628
Polymers125,9238
Non-polymers1,87420
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area29320 Å2
ΔGint-279 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.964, 80.964, 72.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11B-442-

HOH

21C-439-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A OCTAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
putative extracellular heme-binding protein


Mass: 15740.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio piger (bacteria) / Strain: ATCC 29098 / Gene: DESPIG_02683, ZP_03312748.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B6WX57
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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 RESIDUES 23-169 OF 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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4M ammonium sulfate, 0.1M Bicine pH 9.0, NANODROP, 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: 0.91837,0.97879,0.97812
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978791
30.978121
ReflectionResolution: 1.24→28.625 Å / Num. obs: 131689 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.502 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.24-1.280.5391.7463962209792.2
1.28-1.340.422.2623512995198.2
1.34-1.40.3162.9495412397393
1.4-1.470.2314521492436698.1
1.47-1.560.1535.8535412542798.5
1.56-1.680.1028.5514572489195.2
1.68-1.850.06413.2566322621998.8
1.85-2.120.03422.8532112557196.3
2.12-2.670.02135.3562902556997.5
2.670.01450.6529362486494.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.5.0110refinement
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.24→28.625 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.07 / SU B: 1.226 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.039
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. SULFATE (SO4) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1494 6635 5 %RANDOM
Rwork0.128 ---
obs0.1291 131689 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.66 Å2 / Biso mean: 17.4296 Å2 / Biso min: 7.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.24→28.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 57 559 4756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214767
X-RAY DIFFRACTIONr_bond_other_d0.0010.023266
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9686537
X-RAY DIFFRACTIONr_angle_other_deg0.86838010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26322.558215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7371558
X-RAY DIFFRACTIONr_chiral_restr0.0740.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02971
X-RAY DIFFRACTIONr_mcbond_it1.5232986
X-RAY DIFFRACTIONr_mcbond_other0.89231249
X-RAY DIFFRACTIONr_mcangle_it2.34254866
X-RAY DIFFRACTIONr_scbond_it3.09381781
X-RAY DIFFRACTIONr_scangle_it4.693111604
X-RAY DIFFRACTIONr_rigid_bond_restr1.11638033
X-RAY DIFFRACTIONr_sphericity_free3.9993576
X-RAY DIFFRACTIONr_sphericity_bonded2.38437919
LS refinement shellResolution: 1.241→1.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 475 -
Rwork0.2 9150 -
all-9625 -
obs--98.44 %

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