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- PDB-3u22: Crystal structure of a putative HmuY_like heme binding protein (B... -

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Basic information

Entry
Database: PDB / ID: 3u22
TitleCrystal structure of a putative HmuY_like heme binding protein (BVU_2192) from Bacteroides vulgatus ATCC 8482 at 2.12 A resolution
Componentsputative HmuY_like heme binding protein
KeywordsHEME BINDING PROTEIN / transport / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / HEME-BINDING PROTEIN
Function / homologyHmuY protein / HmuY protein / Unknown ligand / Uncharacterized protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative HmuY_like heme binding protein (BVU_2192) from Bacteroides vulgatus ATCC 8482 at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative HmuY_like heme binding protein
B: putative HmuY_like heme binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,79120
Polymers46,2512
Non-polymers1,54118
Water4,954275
1
A: putative HmuY_like heme binding protein
B: putative HmuY_like heme binding protein
hetero molecules

A: putative HmuY_like heme binding protein
B: putative HmuY_like heme binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,58240
Polymers92,5014
Non-polymers3,08136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area14340 Å2
ΔGint-317 kcal/mol
Surface area31670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.415, 128.415, 110.785
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A39 - 144
2116B39 - 144
1216A149 - 220
2216B149 - 220
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative HmuY_like heme binding protein


Mass: 23125.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_2192 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L2D9

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Non-polymers , 5 types, 293 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

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 20-220 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M bicine pH 9, 1.6M ammonium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97922,0.97889
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal 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
20.979221
30.978891
ReflectionResolution: 2.12→78.487 Å / Num. all: 60126 / Num. obs: 60126 / % possible obs: 100 % / Redundancy: 5.7 % / Rsym value: 0.118 / Net I/σ(I): 9.6
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.12-2.235.80.74990086741.019100
2.23-2.375.80.84731482240.672100
2.37-2.535.81.54482877740.476100
2.53-2.745.81.64159472100.317100
2.74-35.83.93841666580.183100
3-3.355.86.13480460390.109100
3.35-3.875.78.63082953620.067100
3.87-4.745.79.42603145560.05100
4.74-6.75.612.22016635740.046100
6.7-78.4875.312.81097420550.03999.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.15data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.12→78.487 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.417 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.09
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. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 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 ION (SO4) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 6. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED. 7. RESIDUE MSE172 FROM BOTH CHAINS ARE LOCATED IN THE SAME REGION AND THEREFORE IT IS DIFFICULT TO MODEL THEIR SIDECHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1724 3029 5 %RANDOM
Rwork0.1647 ---
obs0.1651 60066 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 122.88 Å2 / Biso mean: 48.5786 Å2 / Biso min: 28 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20.95 Å20 Å2
2--1.9 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.12→78.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 104 275 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023090
X-RAY DIFFRACTIONr_bond_other_d0.0030.022010
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9584206
X-RAY DIFFRACTIONr_angle_other_deg1.34334888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4085376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67124.286147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17115484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4841515
X-RAY DIFFRACTIONr_chiral_restr0.1110.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023419
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02652
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2307 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.375
LOOSE THERMAL3.0510
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 202 -
Rwork0.301 3959 -
all-4161 -
obs--99.69 %
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)
11.12860.9363-0.68480.9016-0.63863.0196-0.0235-0.0546-0.0545-0.0367-0.0041-0.0432-0.09970.05930.02760.0434-0.0014-0.00920.03670.01950.0618-0.976.4938.258
22.65971.6309-0.09281.5094-0.30161.3401-0.24050.3192-0.084-0.19940.1777-0.05030.130.06040.06290.0854-0.06850.01510.1345-0.03190.0158-27.86654.8312.801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 220
2X-RAY DIFFRACTION2B38 - 220

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