HEADER STRUCTURAL PROTEIN 12-JAN-04 1S35 TITLE CRYSTAL STRUCTURE OF REPEATS 8 AND 9 OF HUMAN ERYTHROID SPECTRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECTRIN BETA CHAIN, ERYTHROCYTE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: REPEATS 8 AND 9; COMPND 5 SYNONYM: BETA-I SPECTRIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SPTB, SPTB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23D KEYWDS TWO REPEATS OF SPECTRIN, ALPHA HELICAL LINKER REGION, 3-HELIX COILED- KEYWDS 2 COILS, BETA SPECTRIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KUSUNOKI,R.I.MACDONALD,A.MONDRAGON REVDAT 4 14-FEB-24 1S35 1 REMARK REVDAT 3 27-OCT-21 1S35 1 REMARK SEQADV REVDAT 2 24-FEB-09 1S35 1 VERSN REVDAT 1 20-APR-04 1S35 0 JRNL AUTH H.KUSUNOKI,R.I.MACDONALD,A.MONDRAGON JRNL TITL STRUCTURAL INSIGHTS INTO THE STABILITY AND FLEXIBILITY OF JRNL TITL 2 UNUSUAL ERYTHROID SPECTRIN REPEATS JRNL REF STRUCTURE V. 12 645 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15062087 JRNL DOI 10.1016/J.STR.2004.02.022 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15134 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 SET) : 0.222 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 746 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 100 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1679 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.88000 REMARK 3 B22 (A**2) : 10.88000 REMARK 3 B33 (A**2) : -21.76000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.553 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.456 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.037 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.558 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 45.45 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796,0.9794,0.9642 REMARK 200 MONOCHROMATOR : SILICON MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15165 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30300 REMARK 200 R SYM FOR SHELL (I) : 0.27900 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP, SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 0.3 M AMMONIUM REMARK 280 SULFATE, 1.2-1.3 M LITHIUM SULFATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.77400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 61.07550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.07550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.38700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.07550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 61.07550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.16100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.07550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.07550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.38700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 61.07550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.07550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.16100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 24.77400 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 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 MET A 1062 REMARK 465 LEU A 1274 REMARK 465 GLU A 1275 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 DBREF 1S35 A 1063 1275 UNP P11277 SPTB1_HUMAN 1063 1275 SEQADV 1S35 MET A 1062 UNP P11277 CLONING ARTIFACT SEQADV 1S35 GLU A 1063 UNP P11277 LEU 1063 ENGINEERED MUTATION SEQRES 1 A 214 MET GLU GLN ALA PHE LEU GLN ASP LEU ASP ASP PHE GLN SEQRES 2 A 214 ALA TRP LEU SER ILE THR GLN LYS ALA VAL ALA SER GLU SEQRES 3 A 214 ASP MET PRO GLU SER LEU PRO GLU ALA GLU GLN LEU LEU SEQRES 4 A 214 GLN GLN HIS ALA GLY ILE LYS ASP GLU ILE ASP GLY HIS SEQRES 5 A 214 GLN ASP SER TYR GLN ARG VAL LYS GLU SER GLY GLU LYS SEQRES 6 A 214 VAL ILE GLN GLY GLN THR ASP PRO GLU TYR LEU LEU LEU SEQRES 7 A 214 GLY GLN ARG LEU GLU GLY LEU ASP THR GLY TRP ASP ALA SEQRES 8 A 214 LEU GLY ARG MET TRP GLU SER ARG SER HIS THR LEU ALA SEQRES 9 A 214 GLN CYS LEU GLY PHE GLN GLU PHE GLN LYS ASP ALA LYS SEQRES 10 A 214 GLN ALA GLU ALA ILE LEU SER ASN GLN GLU TYR THR LEU SEQRES 11 A 214 ALA HIS LEU GLU PRO PRO ASP SER LEU GLU ALA ALA GLU SEQRES 12 A 214 ALA GLY ILE ARG LYS PHE GLU ASP PHE LEU GLY SER MET SEQRES 13 A 214 GLU ASN ASN ARG ASP LYS VAL LEU SER PRO VAL ASP SER SEQRES 14 A 214 GLY ASN LYS LEU VAL ALA GLU GLY ASN LEU TYR SER ASP SEQRES 15 A 214 LYS ILE LYS GLU LYS VAL GLN LEU ILE GLU ASP ARG HIS SEQRES 16 A 214 ARG LYS ASN ASN GLU LYS ALA GLN GLU ALA SER VAL LEU SEQRES 17 A 214 LEU ARG ASP ASN LEU GLU HET SO4 A 300 5 HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *182(H2 O) HELIX 1 1 GLN A 1064 SER A 1086 1 23 HELIX 2 2 SER A 1092 GLN A 1129 1 38 HELIX 3 3 ASP A 1133 HIS A 1193 1 61 HELIX 4 4 SER A 1199 GLU A 1237 1 39 HELIX 5 5 TYR A 1241 ASP A 1272 1 32 SITE 1 AC1 3 ARG A1221 HIS A1256 ASN A1260 SITE 1 AC2 4 ALA A1083 LEU A1099 HIS A1103 ARG A1160 CRYST1 122.151 122.151 49.548 90.00 90.00 90.00 P 41 21 2 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 0.008187 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020182 0.00000