PDB Short entry for 5TO4 HEADER HYDROLASE 16-OCT-16 5TO4 TITLE PHOSPHOLIPASE C GAMMA-1 C-TERMINAL SH2 DOMAIN, SPACEGROUP P212121 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE PHOSPHODIESTERASE COMPND 3 GAMMA-1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 663-759; COMPND 6 SYNONYM: PLC-148,PHOSPHOINOSITIDE PHOSPHOLIPASE C-GAMMA-1, COMPND 7 PHOSPHOLIPASE C-II,PLC-II,PHOSPHOLIPASE C-GAMMA-1,PLC-GAMMA-1; COMPND 8 EC: 3.1.4.11; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: SCATTERED ELECTRON DENSITY WAS ALSO PRESENT FOR AT COMPND 11 LEAST TWO ADDITIONAL POLYMERS, LIKELY LOW MOLECULAR WEIGHT COMPND 12 POLYETHYLENE GLYCOL MOLECULES. HOWEVER, THE MOLECULES COULD NOT BE COMPND 13 FIT INTO THE DENSITY NON-AMBIGUOUSLY AND WERE CONSEQUENTLY OMITTED COMPND 14 FROM THE MODEL. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: PLCG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS SH2, PHOSPHOLIPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.S.WUTTKE,M.A.MCKERCHER REVDAT 4 04-OCT-23 5TO4 1 REMARK REVDAT 3 10-MAY-17 5TO4 1 JRNL REVDAT 2 26-APR-17 5TO4 1 JRNL REVDAT 1 19-APR-17 5TO4 0 JRNL AUTH M.A.MCKERCHER,X.GUAN,Z.TAN,D.S.WUTTKE JRNL TITL MULTIMODAL RECOGNITION OF DIVERSE PEPTIDES BY THE C-TERMINAL JRNL TITL 2 SH2 DOMAIN OF PHOSPHOLIPASE C-GAMMA 1 PROTEIN. JRNL REF BIOCHEMISTRY V. 56 2225 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28376302 JRNL DOI 10.1021/ACS.BIOCHEM.7B00023 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 12291 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 614 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 28.1179 - 2.6980 0.96 3037 157 0.1751 0.2058 REMARK 3 2 2.6980 - 2.1418 0.98 2914 155 0.1930 0.2225 REMARK 3 3 2.1418 - 1.8711 0.97 2879 150 0.1858 0.2550 REMARK 3 4 1.8711 - 1.7000 0.97 2847 152 0.2064 0.2552 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.64 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 : 0.010 885 REMARK 3 ANGLE : 1.021 1195 REMARK 3 CHIRALITY : 0.054 119 REMARK 3 PLANARITY : 0.006 157 REMARK 3 DIHEDRAL : 17.411 545 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 5TO4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 36.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: 4K44 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE (PH 5.5), 22% PEG REMARK 280 1000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 17.01500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.19000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.19000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.01500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.22000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 659 REMARK 465 GLU A 759 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 684 NE CZ NH1 NH2 REMARK 480 LYS A 711 CE NZ REMARK 480 LYS A 749 CG CD CE NZ 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 H ASN A 700 O HOH A 802 1.35 REMARK 500 O HOH A 828 O HOH A 865 1.83 REMARK 500 NH2 ARG A 684 O HOH A 801 1.99 REMARK 500 N ASN A 700 O HOH A 802 2.18 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 ARG A 748 -114.34 48.89 REMARK 500 ASN A 757 -75.91 -113.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 874 DISTANCE = 5.90 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TNW RELATED DB: PDB DBREF 5TO4 A 663 759 UNP P08487 PLCG1_BOVIN 663 759 SEQADV 5TO4 GLY A 659 UNP P08487 EXPRESSION TAG SEQADV 5TO4 SER A 660 UNP P08487 EXPRESSION TAG SEQADV 5TO4 HIS A 661 UNP P08487 EXPRESSION TAG SEQADV 5TO4 MET A 662 UNP P08487 EXPRESSION TAG SEQRES 1 A 101 GLY SER HIS MET HIS GLU SER LYS GLU TRP TYR HIS ALA SEQRES 2 A 101 SER LEU THR ARG ALA GLN ALA GLU HIS MET LEU MET ARG SEQRES 3 A 101 VAL PRO ARG ASP GLY ALA PHE LEU VAL ARG LYS ARG ASN SEQRES 4 A 101 GLU PRO ASN SER TYR ALA ILE SER PHE ARG ALA GLU GLY SEQRES 5 A 101 LYS ILE LYS HIS CYS ARG VAL GLN GLN GLU GLY GLN THR SEQRES 6 A 101 VAL MET LEU GLY ASN SER GLU PHE ASP SER LEU VAL ASP SEQRES 7 A 101 LEU ILE SER TYR TYR GLU LYS HIS PRO LEU TYR ARG LYS SEQRES 8 A 101 MET LYS LEU ARG TYR PRO ILE ASN GLU GLU FORMUL 2 HOH *74(H2 O) HELIX 1 AA1 HIS A 661 LYS A 666 5 6 HELIX 2 AA2 THR A 674 ARG A 684 1 11 HELIX 3 AA3 SER A 733 HIS A 744 1 12 SHEET 1 AA1 6 TYR A 669 HIS A 670 0 SHEET 2 AA1 6 ALA A 690 LYS A 695 1 O VAL A 693 N HIS A 670 SHEET 3 AA1 6 SER A 701 ALA A 708 -1 O ALA A 703 N ARG A 694 SHEET 4 AA1 6 LYS A 711 GLU A 720 -1 O LYS A 713 N PHE A 706 SHEET 5 AA1 6 THR A 723 LEU A 726 -1 O THR A 723 N GLU A 720 SHEET 6 AA1 6 SER A 729 PHE A 731 -1 O SER A 729 N LEU A 726 SHEET 1 AA2 3 TYR A 669 HIS A 670 0 SHEET 2 AA2 3 ALA A 690 LYS A 695 1 O VAL A 693 N HIS A 670 SHEET 3 AA2 3 TYR A 754 PRO A 755 1 O TYR A 754 N PHE A 691 CRYST1 34.030 36.440 88.380 90.00 90.00 90.00 P 21 21 21 4 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 0.029386 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011315 0.00000