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- PDB-2j0p: Structure of the haem-chaperone Proteobacteria-protein HemS -

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Basic information

Entry
Database: PDB / ID: 2j0p
TitleStructure of the haem-chaperone Proteobacteria-protein HemS
ComponentsHEMIN TRANSPORT PROTEIN HEMS
KeywordsTRANSPORT PROTEIN / CONFORMATIONAL CHANGES / HAEM / IRON / TRANSPORT / ION TRANSPORT / PROTEOBACTERIA / IRON TRANSPORT / HAEM-BINDING PROTEIN
Function / homology
Function and homology information


Haemin-degrading HemS/ChuX domain / Haemin-degrading HemS.ChuX domain / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / DI(HYDROXYETHYL)ETHER / Hemin transport protein HemS
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchneider, S. / Sharp, K.H. / Barker, P.D. / Paoli, M.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: An Induced Fit Conformational Change Underlies the Binding Mechanism of the Heme Transport Proteobacteria-Protein Hems.
Authors: Schneider, S. / Sharp, K.H. / Barker, P.D. / Paoli, M.
#1: Journal: Acta Crystallogr., Sect.F / Year: 2005
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the Haem-Binding Protein Hems from Yersinia Enterocolitica.
Authors: Schneider, S. / Paoli, M.
History
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMIN TRANSPORT PROTEIN HEMS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6175
Polymers39,2461
Non-polymers1,3714
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.941, 77.593, 114.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEMIN TRANSPORT PROTEIN HEMS / HEMS


Mass: 39245.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: WA-C / Plasmid: PGAT2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31517

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsASN 162 IS ILE IN THE SEQUENCE FILE P31517. COMPARISON OF MULTIPLE SEQUENCE ALIGNMENTS OF HEMS ...ASN 162 IS ILE IN THE SEQUENCE FILE P31517. COMPARISON OF MULTIPLE SEQUENCE ALIGNMENTS OF HEMS HOMOLOGUES AND HEMS FROM Y.ENTEROCOLITICA STRAIN 8081 SEQUENCED AT THE SANGER INSTITUTE, SHOW ASN AT THIS POSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growDetails: 50MM TRIS-HCL PH8.5, 1.8M AMMONIUM SULPHATE, 4% PEG400

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2005 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 36050 / % possible obs: 97.5 % / Observed criterion σ(I): 4 / Redundancy: 11.7 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.4 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U9T

1u9t


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.291 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3, 170-179 AND 342-345 ARE DISORDERED. NE2 OF HIS196 IS COORDINATING THE HAEM-IRON.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1807 5 %RANDOM
Rwork0.192 ---
obs0.194 34237 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.75 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 78 169 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212770
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9833767
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7315334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79924.366142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37615450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3531520
X-RAY DIFFRACTIONr_chiral_restr0.1930.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21152
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21921
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2531.51669
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4722646
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.67131217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0164.51116
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 130
Rwork0.25 2448
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)
18.79070.129-2.66996.4319-1.655610.9365-0.0553-0.4611-0.14470.39290.2602-0.21590.40750.7105-0.2049-0.00870.0643-0.0671-0.0401-0.0130.076427.09265.055914.2701
23.7375-0.90670.53982.92091.10542.31670.108-0.0805-0.41970.08730.06280.02460.2452-0.0214-0.17080.0638-0.02380.023-0.02230.06230.094916.79589.336311.5723
30.9604-0.2274-0.540.7147-0.15030.81330.00680.0294-0.0381-0.02330.00610.099-0.0109-0.0673-0.01280.0346-0.0053-0.00530.0160.00290.047313.87725.00720.8155
419.2368-3.9686-0.359811.26230.46120.0211-0.1999-0.0788-0.3739-0.20020.1453-0.40970.26940.33460.05460.03310.01190.0090.20870.02580.018728.515719.135115.8747
52.09910.3008-0.31913.28080.2141.03690.0109-0.2761-0.11450.1478-0.01050.1267-0.0275-0.0608-0.00030.059-0.00170.00350.06350.03230.05213.64421.017211.3915
60.18230.1775-0.91440.8936-1.82015.78550.03090.1679-0.2899-0.1296-0.01750.18980.328-0.3527-0.01340.01750.0154-0.06510.2258-0.06160.02019.052515.638-20.1541
73.6432-0.3651.47292.15960.88453.89180.22690.0917-0.4097-0.2023-0.2010.06930.218-0.4104-0.02590.04660.0038-0.00030.0975-0.04-0.057919.813.0921-24.0244
81.954-0.5813-0.51051.4680.29951.42920.06560.04570.1479-0.07770.0313-0.2759-0.03310.22-0.09690.0269-0.0120.02220.0336-0.00970.063829.964225.142-9.6798
91.3164-0.2866-0.67431.42960.6741.89670.05790.1798-0.0029-0.1214-0.0279-0.0128-0.0208-0.0555-0.02990.05520.00340.01560.063-0.00090.040724.025720.2061-15.125
106.1788-3.36-1.12955.62682.40183.57930.23930.24340.291-0.5526-0.1773-0.2374-0.41390.0067-0.0620.11910.01030.09270.01610.0579-0.034625.745230.019-23.1752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 20
2X-RAY DIFFRACTION2A21 - 50
3X-RAY DIFFRACTION3A51 - 115
4X-RAY DIFFRACTION4A116 - 123
5X-RAY DIFFRACTION5A124 - 164
6X-RAY DIFFRACTION6A165 - 203
7X-RAY DIFFRACTION7A204 - 228
8X-RAY DIFFRACTION8A229 - 273
9X-RAY DIFFRACTION9A274 - 319
10X-RAY DIFFRACTION10A320 - 341

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