HEADER TRANSFERASE 27-JUL-06 2IZX
TITLE MOLECULAR BASIS OF AKAP SPECIFICITY FOR PKA REGULATORY SUBUNITS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA
COMPND 3 REGULATORY SUBUNIT;
COMPND 4 CHAIN: A, B;
COMPND 5 FRAGMENT: 3-43;
COMPND 6 SYNONYM: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II;
COMPND 7 EC: 2.7.11.11;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: AKAP-IS;
COMPND 11 CHAIN: C
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P1;
SOURCE 9 MOL_ID: 2;
SOURCE 10 SYNTHETIC: YES;
SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 12 ORGANISM_TAXID: 32630
KEYWDS CAMP-BINDING, PHOSPHORYLATION, NUCLEOTIDE-BINDING, PKA,
KEYWDS 2 CAMP, AKAP, ANCHOR, KINASE, ACETYLATION, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.G.GOLD,B.LYGREN,P.DOKURNO,N.HOSHI,G.MCCONNACHIE,K.TASKEN,
AUTHOR 2 C.R.CARLSON,J.D.SCOTT,D.BARFORD
REVDAT 3 08-FEB-17 2IZX 1 HEADER TITLE COMPND SOURCE
REVDAT 3 2 REMARK VERSN FORMUL
REVDAT 2 24-FEB-09 2IZX 1 VERSN
REVDAT 1 08-NOV-06 2IZX 0
JRNL AUTH M.G.GOLD,B.LYGREN,P.DOKURNO,N.HOSHI,G.MCCONNACHIE,
JRNL AUTH 2 K.TASKEN,C.R.CARLSON,J.D.SCOTT,D.BARFORD
JRNL TITL MOLECULAR BASIS OF AKAP SPECIFICITY FOR PKA
JRNL TITL 2 REGULATORY SUBUNITS.
JRNL REF MOL.CELL V. 24 383 2006
JRNL REFN ISSN 1097-2765
JRNL PMID 17081989
JRNL DOI 10.1016/J.MOLCEL.2006.09.006
REMARK 2
REMARK 2 RESOLUTION. 1.3 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.42
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 25468
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) : 0.166
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.194
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1348
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) : 1.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1845
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3160
REMARK 3 BIN FREE R VALUE SET COUNT : 105
REMARK 3 BIN FREE R VALUE : 0.3530
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 800
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 16
REMARK 3 SOLVENT ATOMS : 99
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.24
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.11000
REMARK 3 B22 (A**2) : 0.11000
REMARK 3 B33 (A**2) : -0.01000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.050
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.469
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 828 ; 0.018 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1122 ; 1.805 ; 2.013
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 95 ; 3.787 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;32.064 ;24.048
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 140 ;11.012 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 9.621 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 132 ; 0.144 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 620 ; 0.010 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 464 ; 0.278 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 593 ; 0.324 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 68 ; 0.209 ; 0.200
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): 24 ; 0.166 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.107 ; 0.200
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): 509 ; 2.167 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 800 ; 2.706 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 356 ; 3.927 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 322 ; 5.582 ; 4.500
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 : 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: HYDROGENS HAVE BEEN ADDED IN THE
REMARK 3 RIDING POSITIONS.Q4 IN AKAP-IS IS MODELLED AS ALANINE
REMARK 4
REMARK 4 2IZX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-06.
REMARK 100 THE PDBE ID CODE IS EBI-29512.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JUL-05
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.970
REMARK 200 MONOCHROMATOR : SILICON FILTER
REMARK 200 OPTICS : CYLINDRICAL GRAZING INCIDENCE
REMARK 200 MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26863
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300
REMARK 200 RESOLUTION RANGE LOW (A) : 35.400
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 4.350
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 2.90
REMARK 200 R MERGE FOR SHELL (I) : 0.34000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500
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: RII APO CRYSTAL STRUCTURE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.9
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M TRI-SODIUM CITRATE, 0.1 M
REMARK 280 TRIS-HCL PH 7.5
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 20.67600
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.41850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.62550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.41850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.67600
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.62550
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 ILE A 3
REMARK 465 GLN A 4
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN C 4 CG CD OE1 NE2
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 N ILE A 5 - O HOH A 2002 2.18
REMARK 500 OE2 GLU A 41 - O HOH A 2032 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTD A1044
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTD A1045
DBREF 2IZX A 3 43 UNP P13861 KAP2_HUMAN 3 43
DBREF 2IZX B 3 43 UNP P13861 KAP2_HUMAN 3 43
DBREF 2IZX C 4 21 PDB 2IZX 2IZX 4 21
SEQRES 1 A 41 ILE GLN ILE PRO PRO GLY LEU THR GLU LEU LEU GLN GLY
SEQRES 2 A 41 TYR THR VAL GLU VAL LEU ARG GLN GLN PRO PRO ASP LEU
SEQRES 3 A 41 VAL GLU PHE ALA VAL GLU TYR PHE THR ARG LEU ARG GLU
SEQRES 4 A 41 ALA ARG
SEQRES 1 B 41 ILE GLN ILE PRO PRO GLY LEU THR GLU LEU LEU GLN GLY
SEQRES 2 B 41 TYR THR VAL GLU VAL LEU ARG GLN GLN PRO PRO ASP LEU
SEQRES 3 B 41 VAL GLU PHE ALA VAL GLU TYR PHE THR ARG LEU ARG GLU
SEQRES 4 B 41 ALA ARG
SEQRES 1 C 18 GLN ILE GLU TYR LEU ALA LYS GLN ILE VAL ASP ASN ALA
SEQRES 2 C 18 ILE GLN GLN ALA LYS
HET DTD A1044 8
HET DTD A1045 8
HETNAM DTD DITHIANE DIOL
FORMUL 4 DTD 2(C4 H8 O2 S2)
FORMUL 6 HOH *99(H2 O)
HELIX 1 1 GLY A 8 GLN A 24 1 17
HELIX 2 2 ASP A 27 ARG A 43 1 17
HELIX 3 3 GLY B 8 GLN B 24 1 17
HELIX 4 4 ASP B 27 ALA B 42 1 16
HELIX 5 5 GLN C 4 LYS C 21 1 18
SITE 1 AC1 8 GLN A 23 PHE A 31 GLU A 34 TYR A 35
SITE 2 AC1 8 ARG A 38 DTD A1045 HOH A2037 GLN B 23
SITE 1 AC2 7 ARG A 38 LEU A 39 DTD A1044 HOH A2038
SITE 2 AC2 7 HOH A2039 GLN B 23 ARG B 38
CRYST1 41.352 45.251 56.837 90.00 90.00 90.00 P 21 21 21 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 0.024183 0.000000 0.000000 0.00000
SCALE2 0.000000 0.022099 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017594 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
