PDB Short entry for 1BKR HEADER ACTIN-BINDING 10-JUL-98 1BKR TITLE CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANGSTROM TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECTRIN BETA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: F-ACTIN BINDING DOMAIN RESIDUES 173 - 281; COMPND 5 SYNONYM: CALPONIN HOMOLOGY (CH) DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: NON-ERYTHROCYTE; SOURCE 6 CELLULAR_LOCATION: CYTOSKELETAL PROTEIN; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS FILAMENTOUS ACTIN-BINDING DOMAIN, CYTOSKELETON, ACTIN-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.DJINOVIC CARUGO,S.BANUELOS,M.SARASTE REVDAT 7 07-FEB-24 1BKR 1 REMARK REVDAT 6 24-FEB-09 1BKR 1 VERSN REVDAT 5 01-APR-03 1BKR 1 JRNL REVDAT 4 03-MAY-99 1BKR 1 AUTHOR REVDAT 3 26-FEB-99 1BKR 1 JRNL REVDAT 2 16-SEP-98 1BKR 3 SOURCE COMPND REMARK TITLE REVDAT 2 2 3 SEQRES DBREF AUTHOR KEYWDS REVDAT 2 3 3 SCALE HEADER REVDAT 1 15-JUL-98 1BKR 0 JRNL AUTH S.BANUELOS,M.SARASTE,K.D.CARUGO JRNL TITL STRUCTURAL COMPARISONS OF CALPONIN HOMOLOGY DOMAINS: JRNL TITL 2 IMPLICATIONS FOR ACTIN BINDING. JRNL REF STRUCTURE V. 6 1419 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9817844 JRNL DOI 10.1016/S0969-2126(98)00141-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.D.CARUGO,S.BANUELOS,M.SARASTE REMARK 1 TITL CRYSTAL STRUCTURE OF A CALPONIN HOMOLOGY DOMAIN REMARK 1 REF NAT.STRUCT.BIOL. V. 4 175 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.C.GOLDSMITH,N.POKALA,W.SHEN,A.A.FEDOROV,P.MATSUDAIRA, REMARK 1 AUTH 2 S.C.ALMO REMARK 1 TITL THE STRUCTURE OF AN ACTIN-CROSSLINKING DOMAIN FROM HUMAN REMARK 1 TITL 2 FIMBRIN REMARK 1 REF NAT.STRUCT.BIOL. V. 4 708 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.141 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3092 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 42149 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.128 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 35489 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 887 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1081.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9858 REMARK 3 NUMBER OF RESTRAINTS : 11588 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.022 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.024 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.137 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.010 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.135 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.100 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) FROM 0.225 TO 0.187. ESTIMATED OVERALL COORDINATE REMARK 3 ERROR (FROM LUZZATTI PLOT): 0.05 (ASSUMING PERFECT DATA). REMARK 4 REMARK 4 1BKR 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_1000171869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88830 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42236 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 0.2 M REMARK 280 SODIUM ACETATE 0.1 M SODIUM CACODYLATE PH 6.6 PEG8K 30% (W/V) 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 26.97650 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 300 REMARK: SPECTRIN IS A HETEROTETRAMER CONSISTING OF 2 ALPHA AND 2 REMARK 300 BETA CHAINS. CALPONIN HOMOLOGY DOMAIN IS AT THE N-TERMINAL REMARK 300 PART OF THE BETA CHAIN. 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 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 LYS A 1 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 LYS A 5 CG NZ REMARK 480 PRO A 20 CG REMARK 480 ARG A 32 NH1 NH2 REMARK 480 GLN A 64 CD OE1 NE2 REMARK 480 LYS A 78 CD NZ REMARK 480 LYS A 93 NZ REMARK 480 LYS A 108 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 NH1 ARG A 32 O HOH A 1095 1.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 32 NE ARG A 32 CZ 0.105 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 ARG A 32 CD - NE - CZ ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 32 NH1 - CZ - NH2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 52 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 THR A 77 CA - CB - OG1 ANGL. DEV. = 14.9 DEGREES REMARK 500 THR A 101 N - CA - CB ANGL. DEV. = -21.7 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 THR A 28 -91.83 -135.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BKR A 1 109 UNP Q01082 SPTB2_HUMAN 172 280 SEQRES 1 A 109 LYS LYS SER ALA LYS ASP ALA LEU LEU LEU TRP CYS GLN SEQRES 2 A 109 MET LYS THR ALA GLY TYR PRO ASN VAL ASN ILE HIS ASN SEQRES 3 A 109 PHE THR THR SER TRP ARG ASP GLY MET ALA PHE ASN ALA SEQRES 4 A 109 LEU ILE HIS LYS HIS ARG PRO ASP LEU ILE ASP PHE ASP SEQRES 5 A 109 LYS LEU LYS LYS SER ASN ALA HIS TYR ASN LEU GLN ASN SEQRES 6 A 109 ALA PHE ASN LEU ALA GLU GLN HIS LEU GLY LEU THR LYS SEQRES 7 A 109 LEU LEU ASP PRO GLU ASP ILE SER VAL ASP HIS PRO ASP SEQRES 8 A 109 GLU LYS SER ILE ILE THR TYR VAL VAL THR TYR TYR HIS SEQRES 9 A 109 TYR PHE SER LYS MET FORMUL 2 HOH *208(H2 O) HELIX 1 1 SER A 3 LYS A 15 1 13 HELIX 2 2 THR A 29 TRP A 31 5 3 HELIX 3 3 MET A 35 HIS A 44 1 10 HELIX 4 4 PRO A 46 LEU A 48 5 3 HELIX 5 5 PHE A 51 LYS A 53 5 3 HELIX 6 6 ALA A 59 LEU A 74 1 16 HELIX 7 7 PRO A 82 ILE A 85 1 4 HELIX 8 8 GLU A 92 PHE A 106 1 15 CRYST1 31.650 53.953 32.354 90.00 105.48 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 0.031596 0.000000 0.008750 0.00000 SCALE2 0.000000 0.018535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032072 0.00000