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- PDB-3nu1: Structure of holo form of a periplasmic heme binding protein -

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Basic information

Entry
Database: PDB / ID: 3nu1
TitleStructure of holo form of a periplasmic heme binding protein
ComponentsHemin-binding periplasmic protein
KeywordsMETAL TRANSPORT / TRANSPORT PROTEIN / ALPHA BETA PROTEIN / RIGID HELICAL BACKBONE / SUBSTRATE-BOUND / IRON TRANSPORT / HEME TRANSPORT
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemin-binding periplasmic protein / Hemin-binding periplasmic protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMattle, D. / Goetz, B.A. / Woo, J.S. / Locher, K.P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Two stacked heme molecules in the binding pocket of the periplasmic heme-binding protein HmuT from Yersinia pestis.
Authors: Mattle, D. / Zeltina, A. / Woo, J.S. / Goetz, B.A. / Locher, K.P.
History
DepositionJul 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Hemin-binding periplasmic protein
B: Hemin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1386
Polymers53,6722
Non-polymers2,4664
Water79344
1
A: Hemin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0693
Polymers26,8361
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0693
Polymers26,8361
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 89.240, 288.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Hemin-binding periplasmic protein


Mass: 26835.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: Antiqua / Gene: HMUT, Y0541, YPA_4001, YPO0281, YP_0436 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q1C0R0, UniProt: A0A0E1NWS3*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13% (w/v) PEG 4000, 200mM Mg-acetate, 100mM Na-cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 283K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9788, 0.9184, 0.9796, 0.9794
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.91841
30.97961
40.97941
ReflectionResolution: 2.3→30 Å / Num. obs: 31308 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 71.846 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.360.5651.5483.185237227422031.56796.9
2.36-2.420.3841.1414.388906218721861.155100
2.42-2.490.2830.8535.887579217021700.863100
2.49-2.570.1950.5998.282879206620660.606100
2.57-2.650.1360.40911.779901203920390.414100
2.65-2.750.1220.32714.172764195919590.332100
2.75-2.850.0890.25118.173327190919080.25499.9
2.85-2.970.0590.17225.673326185318530.174100
2.97-3.10.0360.11936.271582175217520.12100
3.1-3.250.0280.09145.668595170017000.092100
3.25-3.430.0190.07156.564938162916290.071100
3.43-3.630.0150.05966.958730151815180.06100
3.63-3.880.0130.05472.252991147414740.054100
3.88-4.20.0120.04978.247523135513550.05100
4.2-4.60.010.04684.946785126512650.046100
4.6-5.140.0090.0458943979115411540.045100
5.14-5.930.0090.04586.938596104010390.04599.9
5.93-7.270.0090.04485.7302668898880.04599.9
7.27-10.280.0080.03788.4243357297290.038100
10.280.0070.03690.2137664474210.03794.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.645 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8099 / SU ML: 0.41 / σ(F): 1.99 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1568 6.39 %Random
Rwork0.1956 ---
obs0.1983 24543 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.68 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 312.62 Å2 / Biso mean: 81.4639 Å2 / Biso min: 32.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.5355 Å2-0 Å2-0 Å2
2--2.5355 Å20 Å2
3----5.0711 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 172 44 3964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053998
X-RAY DIFFRACTIONf_angle_d0.9985482
X-RAY DIFFRACTIONf_chiral_restr0.05624
X-RAY DIFFRACTIONf_plane_restr0.004694
X-RAY DIFFRACTIONf_dihedral_angle_d15.2541456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.58930.29471520.247622272379
2.5893-2.69290.29481520.228122342386
2.6929-2.81540.32221530.250722432396
2.8154-2.96370.32591540.257922612415
2.9637-3.14920.30171540.240222542408
3.1492-3.3920.241550.223122632418
3.392-3.73280.23751570.19923042461
3.7328-4.27160.23311580.1823052463
4.2716-5.37650.21451610.15923542515
5.3765-29.64670.19021720.163225302702
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)
11.75190.89560.00292.55640.68491.75510.04380.51580.0404-0.26220.2110.2545-0.2005-0.1281-0.19110.2701-0.05140.05760.5681-0.10440.4219-2.931656.80125.8291
22.7739-0.21380.63270.9181-0.25031.82070.43290.5838-0.8176-0.0620.1133-0.23970.04861.037-0.53250.13060.0346-0.09380.7764-0.58960.76591.445119.819-17.7649
31.7991-3.44680.47197.13830.91796.33180.661-0.01480.3693-0.4103-0.0278-1.71110.67011.1091-0.77490.42680.05170.13190.5344-0.32450.68235.778951.059910.3259
46.4734-7.08751.10258.109-1.81221.34130.780.4731-2.8428-0.0650.34811.36350.3410.0288-0.97930.45170.1704-0.17321.0212-0.25650.9654-7.229814.8106-13.1987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 26:279)A26 - 279
2X-RAY DIFFRACTION2(chain B and resid 26:279)B26 - 279
3X-RAY DIFFRACTION3A1 - 2
4X-RAY DIFFRACTION4B1 - 2

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