HEADER HYDROLASE 15-NOV-04 1Y0M
TITLE CRYSTAL STRUCTURE OF OF THE SH3 DOMAIN OF PHOSPHOLIPASE C GAMMA-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE
COMPND 3 GAMMA 1;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: SH3 DOMAIN: SEQUENCE DATABASE RESIDUES 791-851;
COMPND 6 SYNONYM: PHOSPHOINOSITIDE PHOSPHOLIPASE C, PLC-GAMMA-1, PHOSPHOLIPASE
COMPND 7 C-GAMMA-1, PLC-II, PLC-148;
COMPND 8 EC: 3.1.4.11;
COMPND 9 ENGINEERED: YES;
COMPND 10 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: NORWAY RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 GENE: PLCG1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1
KEYWDS SH3 DOMAIN, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.MARIUZZA,C.SANGWOO
REVDAT 5 14-FEB-24 1Y0M 1 REMARK
REVDAT 4 20-OCT-21 1Y0M 1 SEQADV
REVDAT 3 11-OCT-17 1Y0M 1 REMARK
REVDAT 2 24-FEB-09 1Y0M 1 VERSN
REVDAT 1 21-FEB-06 1Y0M 0
JRNL AUTH R.MARIUZZA,C.SANGWOO
JRNL TITL CRYSTAL STRUCTURE OF OF THE SH3 DOMAIN OF PHOSPHOLIPASE C
JRNL TITL 2 GAMMA-1
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 3 NUMBER OF REFLECTIONS : 15999
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.151
REMARK 3 FREE R VALUE : 0.177
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 808
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23
REMARK 3 REFLECTION IN BIN (WORKING SET) : 888
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.1910
REMARK 3 BIN FREE R VALUE SET COUNT : 48
REMARK 3 BIN FREE R VALUE : 0.3380
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 508
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 122
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.50
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.05000
REMARK 3 B22 (A**2) : -0.76000
REMARK 3 B33 (A**2) : -0.26000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.36000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.598
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 532 ; 0.010 ; NULL
REMARK 3 BOND LENGTHS OTHERS (A): 449 ; 0.002 ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 714 ; 1.291 ; NULL
REMARK 3 BOND ANGLES OTHERS (DEGREES): 1059 ; 0.787 ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 60 ; 6.459 ; NULL
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 69 ; 0.080 ; NULL
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 589 ; 0.007 ; NULL
REMARK 3 GENERAL PLANES OTHERS (A): 114 ; 0.001 ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 82 ; 0.222 ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 517 ; 0.249 ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 304 ; 0.083 ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 78 ; 0.238 ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 17 ; 0.134 ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): 64 ; 0.232 ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 39 ; 0.160 ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 302 ; 0.964 ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 484 ; 1.526 ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 230 ; 1.815 ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 230 ; 2.725 ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1Y0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-04.
REMARK 100 THE DEPOSITION ID IS D_1000030965.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-DEC-03
REMARK 200 TEMPERATURE (KELVIN) : 105
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CHESS
REMARK 200 BEAMLINE : F1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.91
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16059
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.07700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24
REMARK 200 COMPLETENESS FOR SHELL (%) : 79.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.18100
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: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.10
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: TACSIMATE, PH 7.0, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 15.48900
REMARK 290 SMTRY3 2 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 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 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 NZ LYS A 837 O HOH A 122 0.43
REMARK 500 CE LYS A 837 O HOH A 122 1.65
REMARK 500 NZ LYS A 837 O HOH A 120 1.91
REMARK 500 ND2 ASN A 820 O HOH A 88 1.92
REMARK 500 ND2 ASN A 820 O HOH A 42 2.01
REMARK 500 ND2 ASN A 851 O HOH A 87 2.15
REMARK 500 OG1 THR A 791 O HOH A 75 2.18
REMARK 500 NZ LYS A 797 O HOH A 56 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ASP A 801 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 825 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
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 SER A 815 -9.97 88.08
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HSQ RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE SH3 DOMAIN OF PHOSPHOLIPASE C-GAMMA
DBREF 1Y0M A 791 851 UNP P10686 PIG1_RAT 791 851
SEQADV 1Y0M SER A 794 UNP P10686 CYS 794 ENGINEERED MUTATION
SEQRES 1 A 61 THR PHE LYS SER ALA VAL LYS ALA LEU PHE ASP TYR LYS
SEQRES 2 A 61 ALA GLN ARG GLU ASP GLU LEU THR PHE THR LYS SER ALA
SEQRES 3 A 61 ILE ILE GLN ASN VAL GLU LYS GLN ASP GLY GLY TRP TRP
SEQRES 4 A 61 ARG GLY ASP TYR GLY GLY LYS LYS GLN LEU TRP PHE PRO
SEQRES 5 A 61 SER ASN TYR VAL GLU GLU MET ILE ASN
FORMUL 2 HOH *122(H2 O)
SHEET 1 A 5 LYS A 836 PRO A 842 0
SHEET 2 A 5 TRP A 828 TYR A 833 -1 N TRP A 829 O PHE A 841
SHEET 3 A 5 ILE A 817 GLU A 822 -1 N GLN A 819 O ASP A 832
SHEET 4 A 5 VAL A 796 ALA A 798 -1 N VAL A 796 O ILE A 818
SHEET 5 A 5 VAL A 846 GLU A 848 -1 O GLU A 847 N LYS A 797
CRYST1 28.748 30.978 29.753 90.00 92.12 90.00 P 1 21 1 2
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 0.034785 0.000000 0.001288 0.00000
SCALE2 0.000000 0.032281 0.000000 0.00000
SCALE3 0.000000 0.000000 0.033633 0.00000
(ATOM LINES ARE NOT SHOWN.)
END