HEADER TRANSCRIPTION 22-JUL-17 5Y20
TITLE CRYSTAL STRUCTURE OF AL1 PHD FINGER BOUND TO H3K4ME3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHD FINGER PROTEIN ALFIN-LIKE 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PHD FINGER, UNP RESIDUES 185-236;
COMPND 5 SYNONYM: PROTEIN AL1;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: PEPTIDE FROM HISTONE H3;
COMPND 9 CHAIN: P;
COMPND 10 FRAGMENT: H3 PEPTIDE 1-15;
COMPND 11 ENGINEERED: YES;
COMPND 12 OTHER_DETAILS: K4 TRIMETHYLATION
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA;
SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS;
SOURCE 4 ORGANISM_TAXID: 3702;
SOURCE 5 GENE: AL1, AT5G05610, MOP10.15;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_COMMON: HUMAN;
SOURCE 15 ORGANISM_TAXID: 9606;
SOURCE 16 OTHER_DETAILS: CHEMICALLY SYNTHESIZED H3K4AC PEPTIDE
KEYWDS ZINC FINGER, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR S.ZHAO,B.ZHANG,H.LI
REVDAT 2 25-DEC-19 5Y20 1 JRNL
REVDAT 1 24-JAN-18 5Y20 0
JRNL AUTH S.ZHAO,B.ZHANG,M.YANG,J.ZHU,H.LI
JRNL TITL SYSTEMATIC PROFILING OF HISTONE READERS IN ARABIDOPSIS
JRNL TITL 2 THALIANA.
JRNL REF CELL REP V. 22 1090 2018
JRNL REFN ESSN 2211-1247
JRNL PMID 29386129
JRNL DOI 10.1016/J.CELREP.2017.12.099
REMARK 2
REMARK 2 RESOLUTION. 2.41 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX PHENIX.REFINE: 1.9_1692
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.57
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 3233
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.169
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.215
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 13.860
REMARK 3 FREE R VALUE TEST SET COUNT : 448
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 38.5726 - 3.4735 1.00 984 156 0.1517 0.2176
REMARK 3 2 3.4735 - 2.7573 1.00 920 137 0.1751 0.1915
REMARK 3 3 2.7573 - 2.4088 1.00 881 155 0.1672 0.2474
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.080
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 27.61
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 468
REMARK 3 ANGLE : 1.002 632
REMARK 3 CHIRALITY : 0.041 67
REMARK 3 PLANARITY : 0.005 78
REMARK 3 DIHEDRAL : 14.481 167
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5Y20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-17.
REMARK 100 THE DEPOSITION ID IS D_1300004543.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-MAR-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL17U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111)
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3265
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 26.50
REMARK 200 R MERGE (I) : 0.22100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 27.70
REMARK 200 R MERGE FOR SHELL (I) : 0.84400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 2FSA
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8., 3.0M NACL, PH 8.5,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.08200
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.08400
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.08400
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.54100
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.08400
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.08400
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.62300
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.08400
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.08400
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.54100
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.08400
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.08400
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.62300
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.08200
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1100 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 4030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NE2 GLN A 47 O HOH A 201 2.10
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 VAL A 25 -61.68 -93.12
REMARK 500 LYS A 46 -84.28 -82.71
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 7 SG
REMARK 620 2 CYS A 10 SG 107.6
REMARK 620 3 HIS A 31 ND1 107.0 96.4
REMARK 620 4 CYS A 34 SG 117.7 109.3 116.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 23 SG
REMARK 620 2 CYS A 26 SG 109.2
REMARK 620 3 CYS A 50 SG 110.4 111.1
REMARK 620 4 CYS A 53 SG 106.8 109.1 110.2
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues M3L P 4 through
REMARK 800 GLN P 5 bound to THR P 3
DBREF 5Y20 A 4 55 UNP Q9FFF5 ALFL1_ARATH 185 236
DBREF 5Y20 P 1 7 PDB 5Y20 5Y20 1 7
SEQRES 1 A 52 ASP THR LEU CYS GLY SER CYS GLY GLY ASN TYR THR ASN
SEQRES 2 A 52 ASP GLU PHE TRP ILE CYS CYS ASP VAL CYS GLU ARG TRP
SEQRES 3 A 52 TYR HIS GLY LYS CYS VAL LYS ILE THR PRO ALA LYS ALA
SEQRES 4 A 52 GLU SER ILE LYS GLN TYR LYS CYS PRO SER CYS CYS THR
SEQRES 1 P 7 ALA ARG THR M3L GLN THR ALA
HET M3L P 4 12
HET ZN A 101 1
HET ZN A 102 1
HETNAM M3L N-TRIMETHYLLYSINE
HETNAM ZN ZINC ION
FORMUL 2 M3L C9 H21 N2 O2 1+
FORMUL 3 ZN 2(ZN 2+)
FORMUL 5 HOH *28(H2 O)
HELIX 1 AA1 GLY A 32 LYS A 36 1 5
HELIX 2 AA2 THR A 38 SER A 44 1 7
SHEET 1 AA1 3 TRP A 29 HIS A 31 0
SHEET 2 AA1 3 TRP A 20 CYS A 22 -1 N ILE A 21 O TYR A 30
SHEET 3 AA1 3 THR P 3 M3L P 4 -1 O M3L P 4 N TRP A 20
LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.31
LINK SG CYS A 10 ZN ZN A 101 1555 1555 2.37
LINK SG CYS A 23 ZN ZN A 102 1555 1555 2.30
LINK SG CYS A 26 ZN ZN A 102 1555 1555 2.22
LINK ND1 HIS A 31 ZN ZN A 101 1555 1555 2.14
LINK SG CYS A 34 ZN ZN A 101 1555 1555 2.26
LINK SG CYS A 50 ZN ZN A 102 1555 1555 2.34
LINK SG CYS A 53 ZN ZN A 102 1555 1555 2.28
LINK C THR P 3 N M3L P 4 1555 1555 1.33
LINK C M3L P 4 N GLN P 5 1555 1555 1.32
SITE 1 AC1 4 CYS A 7 CYS A 10 HIS A 31 CYS A 34
SITE 1 AC2 4 CYS A 23 CYS A 26 CYS A 50 CYS A 53
SITE 1 AC3 13 THR A 5 CYS A 10 ASN A 13 TYR A 14
SITE 2 AC3 13 PHE A 19 TRP A 20 TRP A 29 HOH A 213
SITE 3 AC3 13 THR P 3 THR P 6 ALA P 7 HOH P 101
SITE 4 AC3 13 HOH P 104
CRYST1 46.168 46.168 70.164 90.00 90.00 90.00 P 41 21 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.021660 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021660 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014252 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
