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- PDB-1z7c: Crystal Structure of Human Placental Lactogen -

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Basic information

Entry
Database: PDB / ID: 1z7c
TitleCrystal Structure of Human Placental Lactogen
ComponentsChorionic somatomammotropin hormone
KeywordsHORMONE/GROWTH FACTOR / four-helix bundle protein / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


positive regulation of growth / animal organ development / growth hormone receptor binding / growth hormone receptor signaling pathway / Prolactin receptor signaling / growth hormone receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / positive regulation of tyrosine phosphorylation of STAT protein / response to nutrient levels / endosome lumen ...positive regulation of growth / animal organ development / growth hormone receptor binding / growth hormone receptor signaling pathway / Prolactin receptor signaling / growth hormone receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / positive regulation of tyrosine phosphorylation of STAT protein / response to nutrient levels / endosome lumen / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / hormone activity / vesicle / endoplasmic reticulum / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chorionic somatomammotropin hormone 2 / Chorionic somatomammotropin hormone 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWalsh, S.T.R. / Kossiakoff, A.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure and Site 1 Binding Energetics of Human Placental Lactogen.
Authors: Walsh, S.T.R. / Kossiakoff, A.A.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorionic somatomammotropin hormone


Theoretical massNumber of molelcules
Total (without water)22,3351
Polymers22,3351
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.504, 30.047, 53.490
Angle α, β, γ (deg.)90.00, 113.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-192-

HOH

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Components

#1: Protein Chorionic somatomammotropin hormone / Choriomammotropin / Lactogen


Mass: 22335.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSH1 / Plasmid: Custom / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01243, UniProt: P0DML2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium phosphate, PEG 3400, sodium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D11
SYNCHROTRONAPS 19-ID20.9792934, 0.97912954, 0.95373385
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 3, 2001
CUSTOM-MADE2CCDJul 17, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Si (111) double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97929341
30.979129541
40.953733851
ReflectionResolution: 1.9→30 Å / Num. obs: 13322 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.503 / % possible all: 70.6

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.7 Å / D res low: 15 Å / FOM : 0.48 / Reflection: 4723
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97933.5-9.9
13 wavelength20.97916-7.6
13 wavelength30.95373.6-2.9
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se23.6710.14700.2030.479
2Se600.5730.4840.370.628
3Se52.5550.1030.440.3010.505
4Se600.3310.2890.0340.615
5Se600.180.2390.3990.507
Phasing MAD shell
Resolution (Å)FOM Reflection
8.55-150.6285
5.8-8.550.63414
4.65-5.80.59503
3.99-4.650.55596
3.55-3.990.54656
3.23-3.550.45720
2.98-3.230.4772
2.78-2.980.32777
Phasing dmFOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.68 / Reflection: 4723 / Reflection acentric: 4165 / Reflection centric: 558
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-14.9430.90.940.8219314053
4.8-7.70.880.890.82659543116
3.9-4.80.870.880.85804702102
3.4-3.90.80.810.7381472193
2.9-3.40.610.620.4914161289127
2.7-2.90.440.450.3483777067

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
RESOLVE2.06phasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RefinementMethod to determine structure: MAD / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.418 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26704 1126 9.8 %RANDOM
Rwork0.22939 ---
obs0.23308 10328 98.12 %-
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 mean: 36.324 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.61 Å2
2--1.19 Å20 Å2
3----0.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 0 65 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221347
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1411.9731813
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4065156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48323.97168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.70415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.28159
X-RAY DIFFRACTIONr_chiral_restr0.1590.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02997
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.2662
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2914
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4431.5840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25221285
X-RAY DIFFRACTIONr_scbond_it3.4813594
X-RAY DIFFRACTIONr_scangle_it4.9514.5528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 73 -
Rwork0.286 648 -
obs--85.33 %
Refinement TLS params.Method: refined / Origin x: 12.7971 Å / Origin y: 0.1042 Å / Origin z: 8.6682 Å
111213212223313233
T-0.0404 Å2-0.0163 Å2-0.0088 Å2--0.0536 Å20.0059 Å2---0.0207 Å2
L1.1255 °2-0.4078 °2-0.7467 °2-0.8713 °20.8567 °2--2.4429 °2
S-0.0668 Å °-0.0432 Å °-0.1178 Å °0.0133 Å °-0.0821 Å °0.0464 Å °0.0146 Å °-0.1507 Å °0.149 Å °
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:gol.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:peg.top
X-RAY DIFFRACTION4CNS_TOPPAR:gol.param
X-RAY DIFFRACTION5CNS_TOPPAR:peg.param

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