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- PDB-3luz: Crystal structure of extragenic suppressor protein suhB from Bart... -

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Basic information

Entry
Database: PDB / ID: 3luz
TitleCrystal structure of extragenic suppressor protein suhB from Bartonella henselae, via combined iodide SAD molecular replacement
ComponentsExtragenic suppressor protein suhB
KeywordsHYDROLASE / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Bartonella / cat scratch disease / iodide phasing
Function / homology
Function and homology information


: / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / metal ion binding
Similarity search - Function
Inositol monophosphatase SuhB-like / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Inositol monophosphatase SuhB-like / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Inositol-1-monophosphatase / Inositol-1-monophosphatase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SAD, MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J Struct Funct Genomics / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
History
DepositionFeb 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Extragenic suppressor protein suhB
B: Extragenic suppressor protein suhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,63817
Polymers58,9392
Non-polymers1,69815
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-32 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.540, 81.280, 58.760
Angle α, β, γ (deg.)90.000, 98.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A2 - 261
2116B2 - 261

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Components

#1: Protein Extragenic suppressor protein suhB


Mass: 29469.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: suhB, BH15030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G1Z6, UniProt: A0A0H3M6W8*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24 mg/mL protein in 0.2 M MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 400 soaked into 0.2 M MgCl2, 0.75 M KI, 0.1 M Hepes pH 8.2, 35% PEG 400; crystal tracking ID for growth 206523d2 and 206575a1 for ...Details: 24 mg/mL protein in 0.2 M MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 400 soaked into 0.2 M MgCl2, 0.75 M KI, 0.1 M Hepes pH 8.2, 35% PEG 400; crystal tracking ID for growth 206523d2 and 206575a1 for iodide soak, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 202195 / Rmerge(I) obs: 0.053 / D res high: 2.05 Å / Num. obs: 53910 / % possible obs: 96.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
9.1729.046059610.031
6.489.17114499.610.031
5.296.48145599.310.033
4.585.29175699.410.03
4.14.58196499.510.03
3.744.1216799.310.032
3.473.74233999.210.037
3.243.47253198.910.041
3.063.24271898.810.049
2.93.06285498.510.063
2.762.9300598.410.075
2.652.76308398.110.091
2.542.65323897.910.114
2.452.5433479810.145
2.372.45349197.510.161
2.292.3736149710.196
2.222.29363597.310.222
2.162.22382996.810.275
2.12.16373994.610.335
2.052.1339681.210.396
ReflectionResolution: 2.05→30 Å / Num. obs: 27477 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 38.09 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.26
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 10323 / Num. unique obs: 1738 / % possible all: 82.1

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Phasing

Phasing
Method
MAD
molecular replacement
Phasing MADD res high: 2.05 Å / D res low: 29.04 Å / FOM : 0.551 / FOM acentric: 0.555 / FOM centric: 0.432 / Reflection: 27454 / Reflection acentric: 26410 / Reflection centric: 889
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.69-130.6540.6780.4815713819
8.06-9.690.6070.6210.48820418321
7.05-8.060.6110.6310.38323321419
6.34-7.050.6450.6640.43826824523
5.81-6.340.6590.6870.35929426922
5.4-5.810.6980.7080.48830028315
5.06-5.40.6830.6920.53835633322
4.78-5.060.6780.6930.45834031620
4.54-4.780.6790.6870.50138136218
4.33-4.540.640.6370.69440037921
4.15-4.330.6130.6270.33140438516
3.99-4.150.6590.6640.55344141922
3.85-3.990.610.6190.42743141120
3.72-3.850.6240.630.48243842213
3.61-3.720.610.620.4249746625
3.5-3.610.5930.5980.4248046216
3.4-3.50.6090.6190.38149947720
3.31-3.40.5620.5690.3252550915
3.23-3.310.5690.5670.62950648420
3.15-3.230.5850.5920.42454652420
3.08-3.150.5850.5890.45255053414
3.01-3.080.5830.5840.54656253822
2.95-3.010.5660.5720.38657055315
2.89-2.950.570.5770.37959056721
2.84-2.890.560.5650.39560859216
2.78-2.840.5630.5680.40259357220
2.73-2.780.5510.5560.35561660114
2.69-2.730.5370.5410.4660658419
2.64-2.690.5630.5710.3365963819
2.6-2.640.5490.5530.38665463717
2.56-2.60.5640.5640.52561860710
2.52-2.560.530.5330.42571368924
2.48-2.520.5390.5430.36165663816
2.45-2.480.5060.510.28267365514
2.41-2.450.5350.540.40570768421
2.38-2.410.4910.4910.48171068918
2.35-2.380.4940.4920.5876946819
2.32-2.350.4980.4980.44673871520
2.29-2.320.5210.5250.37173471618
2.26-2.290.4890.4930.33670668816
2.24-2.260.50.5020.38977575418
2.21-2.240.50.5010.33174773411
2.18-2.210.5010.5020.49973971819
2.16-2.180.5050.5070.42679977819
2.14-2.160.4920.4910.53574572613
2.11-2.140.4830.4890.29577975413
2.09-2.110.4830.490.28574370820
2.07-2.090.4760.4820.21971268312
2.05-2.070.4840.4840.28964460811

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: 2qfl

2qfl


Resolution: 2.05→29.04 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.218 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.798 / SU B: 12.615 / SU ML: 0.166 / SU R Cruickshank DPI: 0.227 / SU Rfree: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1395 5.1 %RANDOM
Rwork0.217 ---
obs0.219 27458 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 115.36 Å2 / Biso mean: 57.542 Å2 / Biso min: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.27 Å2
2--2.65 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 15 124 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223597
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9454866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20423.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80315567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2741529
X-RAY DIFFRACTIONr_chiral_restr0.0910.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022745
Refine LS restraints NCSNumber: 1665 / Type: LOOSE POSITIONAL / Rms dev position: 0.34 Å / Weight position: 5
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 93 -
Rwork0.322 1639 -
all-1732 -
obs--82.01 %
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)
10.52480.1099-0.5142-0.049-0.02411.4251-0.0382-0.02930.1095-0.02160.03340.01080.0201-0.09280.00490.06370.0066-0.01240.1146-0.01930.0945-4.65629.911336.0102
20.8135-0.74670.13430.4598-0.38772.0318-0.11750.07910.11040.0976-0.03020.01720.12990.20360.14760.11520.0440.01420.08970.05010.0467.2341.85629.9334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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