PDB Short entry for 1DEG HEADER CALCIUM-BINDING PROTEIN 07-JUN-93 1DEG TITLE THE LINKER OF DES-GLU84 CALMODULIN IS BENT AS SEEN IN THE CRYSTAL TITLE 2 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: CLASSIFIED KEYWDS CALCIUM-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR S.RAGHUNATHAN,R.CHANDROSS,B.P.CHENG,A.PERSECHINI,S.E.SOBOTTK, AUTHOR 2 R.H.KRETSINGER REVDAT 3 07-FEB-24 1DEG 1 REMARK SEQADV REVDAT 2 24-FEB-09 1DEG 1 VERSN REVDAT 1 31-MAY-94 1DEG 0 JRNL AUTH S.RAGHUNATHAN,R.J.CHANDROSS,B.P.CHENG,A.PERSECHINI, JRNL AUTH 2 S.E.SOBOTTKA,R.H.KRETSINGER JRNL TITL THE LINKER OF DES-GLU84-CALMODULIN IS BENT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 90 6869 1993 JRNL REFN ISSN 0027-8424 JRNL PMID 8341712 JRNL DOI 10.1073/PNAS.90.14.6869 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.KATAOKA,J.F.HEAD,A.PERSECHINI,R.H.KRETSINGER,D.M.ENGELMAN REMARK 1 TITL SMALL-ANGLE X-RAY SCATTERING STUDIES OF CALMODULIN MUTANTS REMARK 1 TITL 2 WITH DELETIONS IN THE LINKER REGION OF THE CENTRAL HELIX REMARK 1 TITL 3 INDICATE THAT THE LINKER REGION RETAINS A PREDOMINANTLY REMARK 1 TITL 4 A-HELICAL CONFORMATION REMARK 1 REF BIOCHEMISTRY V. 30 1188 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.PERSECHINI,R.H.KRETSINGER,T.N.DAVIS REMARK 1 TITL CALMODULINS WITH DELETIONS IN THE CENTRAL HELIX FUNCTIONALLY REMARK 1 TITL 2 REPLACE THE NATIVE PROTEIN IN YEAST CELLS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 88 449 1991 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.PERSECHINI,D.K.BLUMENTHAL,H.W.JARRETT,C.B.KLEE,D.O.HARDY, REMARK 1 AUTH 2 R.H.KRETSINGER REMARK 1 TITL THE EFFECTS OF DELETIONS IN THE CENTRAL HELIX OF CALMODULIN REMARK 1 TITL 2 ON ENZYME ACTIVATION AND PEPTIDE BINDING REMARK 1 REF J.BIOL.CHEM. V. 264 8052 1989 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.PERSECHINI,R.H.KRETSINGER REMARK 1 TITL THE CENTRAL HELIX OF CALMODULIN FUNCTIONS AS A FLEXIBLE REMARK 1 TITL 2 TETHER REMARK 1 REF J.BIOL.CHEM. V. 263 12175 1988 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 5 REMARK 1 AUTH A.PERSECHINI,R.H.KRETSINGER REMARK 1 TITL TOWARD A MODEL OF THE CALMODULIN-MYOSIN LIGHT CHAIN KINASE REMARK 1 TITL 2 COMPLEX: IMPLICATIONS OF CALMODULIN FUNCTION REMARK 1 REF J.CARDIOVASC.PHARMACOL. V. 12 1 1988 REMARK 1 REFN ISSN 0160-2446 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.030 REMARK 3 BOND ANGLES (DEGREES) : 5.490 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DEG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172754. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 22.65000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.95000 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 300 REMARK: THERE IS AN APPROXIMATE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS REMARK 300 ROUGHLY PARALLEL TO B, RELATING DOMAIN I, (RESIDUES 12 - REMARK 300 74) AND DOMAIN II (RESIDUES 85 - 147). THE TRANSFORMATION REMARK 300 PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE REMARK 300 COORDINATES FOR DOMAIN I WHEN APPLIED TO DOMAIN II. 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 650 REMARK 650 HELIX REMARK 650 THERE IS A BEND OF 40 DEGREES BETWEEN THE F2 HELIX RESIDUES REMARK 650 66 - 76, AND THE LINKER 77 - 83. THE ANGLE BETWEEN THE REMARK 650 LINKER AND THE E3 HELIX, 85 - 92, IS 85 DEGREES. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: EF1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: EF2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: EF3 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: EF4 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 3 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: CALM_HUMAN REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 ASP 129 ASN 129 DBREF 1DEG A 5 147 UNP P02593 CALM_HUMAN 5 147 SEQADV 1DEG A UNP P02593 GLU 84 DELETION SEQRES 1 A 142 THR GLU GLU GLN ILE ALA GLU PHE LYS GLU ALA PHE SER SEQRES 2 A 142 LEU PHE ASP LYS ASP GLY ASP GLY THR ILE THR THR LYS SEQRES 3 A 142 GLU LEU GLY THR VAL MET ARG SER LEU GLY GLN ASN PRO SEQRES 4 A 142 THR GLU ALA GLU LEU GLN ASP MET ILE ASN GLU VAL ASP SEQRES 5 A 142 ALA ASP GLY ASN GLY THR ILE ASP PHE PRO GLU PHE LEU SEQRES 6 A 142 THR MET MET ALA ARG LYS MET LYS ASP THR ASP SER GLU SEQRES 7 A 142 GLU ILE ARG GLU ALA PHE ARG VAL PHE ASP LYS ASP GLY SEQRES 8 A 142 ASN GLY TYR ILE SER ALA ALA GLU LEU ARG HIS VAL MET SEQRES 9 A 142 THR ASN LEU GLY GLU LYS LEU THR ASP GLU GLU VAL ASP SEQRES 10 A 142 GLU MET ILE ARG GLU ALA ASN ILE ASP GLY ASP GLY GLN SEQRES 11 A 142 VAL ASN TYR GLU GLU PHE VAL GLN MET MET THR ALA HET CA A 1 1 HET CA A 2 1 HET CA A 3 1 HET CA A 4 1 HETNAM CA CALCIUM ION FORMUL 2 CA 4(CA 2+) HELIX 1 H1 THR A 5 PHE A 19 1 15 HELIX 2 H2 THR A 29 SER A 38 1 10 HELIX 3 H3 GLU A 45 VAL A 55 1 11 HELIX 4 H4 PHE A 65 ASP A 80 1 16 HELIX 5 H5 ARG A 86 PHE A 92 1 7 HELIX 6 H6 ALA A 102 ASN A 111 1 10 HELIX 7 H7 ASP A 118 ALA A 128 1 11 HELIX 8 H8 TYR A 138 ALA A 147 1 10 SHEET 1 BET 2 THR A 26 THR A 28 0 SHEET 2 BET 2 THR A 62 ASP A 64 -1 SHEET 1 BT2 2 TYR A 99 SER A 101 0 SHEET 2 BT2 2 GLN A 135 ASN A 137 -1 SITE 1 EF1 12 ASP A 20 LYS A 21 ASP A 22 GLY A 23 SITE 2 EF1 12 ASP A 24 GLY A 25 THR A 26 ILE A 27 SITE 3 EF1 12 THR A 28 THR A 29 LYS A 30 GLU A 31 SITE 1 EF2 12 ASP A 56 ALA A 57 ASP A 58 GLY A 59 SITE 2 EF2 12 ASN A 60 GLY A 61 THR A 62 ILE A 63 SITE 3 EF2 12 ASP A 64 PHE A 65 PRO A 66 GLU A 67 SITE 1 EF3 12 ASP A 93 LYS A 94 ASP A 95 GLY A 96 SITE 2 EF3 12 ASN A 97 GLY A 98 TYR A 99 ILE A 100 SITE 3 EF3 12 SER A 101 ALA A 102 ALA A 103 GLU A 104 SITE 1 EF4 12 ASN A 129 ILE A 130 ASP A 131 GLY A 132 SITE 2 EF4 12 ASP A 133 GLY A 134 GLN A 135 VAL A 136 SITE 3 EF4 12 ASN A 137 TYR A 138 GLU A 139 GLU A 140 SITE 1 AC1 1 ILE A 27 SITE 1 AC2 1 ILE A 100 CRYST1 45.300 49.900 62.400 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 0.022075 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016026 0.00000 MTRIX1 1 -0.990874 0.076905 0.110695 109.81735 1 MTRIX2 1 0.098889 0.972835 0.209316 -8.59274 1 MTRIX3 1 -0.091590 0.218352 -0.971562 -30.20036 1