HEADER OXYGEN STORAGE/TRANSPORT 09-MAY-05 1X3K TITLE CRYSTAL STRUCTURE OF A HEMOGLOBIN COMPONENT (TA-V) FROM TITLE 2 TOKUNAGAYUSURIKA AKAMUSI COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN COMPONENT V; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOKUNAGAYUSURIKA AKAMUSI; SOURCE 3 ORGANISM_TAXID: 28383; SOURCE 4 TISSUE: LARVAL HEMOLYMPH KEYWDS HEMOGLOBIN, DIPTERA, TOKUNAGAYUSURIKA AKAMUSI, MIDGE LARVA, OXYGEN KEYWDS 2 STORAGE-TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.KUWADA,T.HASEGAWA,S.SATO,I.SATO,K.ISHIKAWA,T.TAKAGI,F.SHISHIKURA REVDAT 5 23-OCT-24 1X3K 1 REMARK LINK REVDAT 4 09-JUN-09 1X3K 1 REVDAT REVDAT 3 24-FEB-09 1X3K 1 VERSN REVDAT 2 02-DEC-08 1X3K 1 JRNL REVDAT 1 24-MAY-05 1X3K 0 JRNL AUTH T.KUWADA,T.HASEGAWA,S.SATO,I.SATO,K.ISHIKAWA,T.TAKAGI, JRNL AUTH 2 F.SHISHIKURA JRNL TITL CRYSTAL STRUCTURES OF TWO HEMOGLOBIN COMPONENTS FROM THE JRNL TITL 2 MIDGE LARVA PROPSILOCERUS AKAMUSI (ORTHOCLADIINAE, DIPTERA). JRNL REF GENE V. 398 29 2007 JRNL REFN ISSN 0378-1119 JRNL PMID 17590288 JRNL DOI 10.1016/J.GENE.2007.02.049 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2000.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,MOLECULAR REMARK 3 : SIMULATIONS (BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1919000.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 20169 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2890 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 312 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1213 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 226 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.39000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : 1.33000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 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) : 17.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 48.50 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : HEM.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : HEM.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20177 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 49.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 6.980 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.91 REMARK 200 R MERGE FOR SHELL (I) : 0.06800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CNX 2000.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM SULFATE, PH 4.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 32.57200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.42750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.57200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.42750 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: 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: 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 ASP A 23 60.47 -150.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HEM A 1001 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1001 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 98 NE2 REMARK 620 2 HEM A1001 NA 86.8 REMARK 620 3 HEM A1001 NB 88.8 90.0 REMARK 620 4 HEM A1001 NC 96.4 176.1 92.2 REMARK 620 5 HEM A1001 ND 93.4 90.9 177.6 86.7 REMARK 620 6 HOH A1002 O 166.6 80.9 96.6 95.6 81.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1001 DBREF 1X3K A 1 152 UNP Q7M422 Q7M422_9DIPT 1 152 SEQRES 1 A 152 ALA PHE VAL GLY LEU SER ASP SER GLU GLU LYS LEU VAL SEQRES 2 A 152 ARG ASP ALA TRP ALA PRO ILE HIS GLY ASP LEU GLN GLY SEQRES 3 A 152 THR ALA ASN THR VAL PHE TYR ASN TYR LEU LYS LYS TYR SEQRES 4 A 152 PRO SER ASN GLN ASP LYS PHE GLU THR LEU LYS GLY HIS SEQRES 5 A 152 PRO LEU ASP GLU VAL LYS ASP THR ALA ASN PHE LYS LEU SEQRES 6 A 152 ILE ALA GLY ARG ILE PHE THR ILE PHE ASP ASN CYS VAL SEQRES 7 A 152 LYS ASN VAL GLY ASN ASP LYS GLY PHE GLN LYS VAL ILE SEQRES 8 A 152 ALA ASP MET SER GLY PRO HIS VAL ALA ARG PRO ILE THR SEQRES 9 A 152 HIS GLY SER TYR ASN ASP LEU ARG GLY VAL ILE TYR ASP SEQRES 10 A 152 SER MET HIS LEU ASP SER THR HIS GLY ALA ALA TRP ASN SEQRES 11 A 152 LYS MET MET ASP ASN PHE PHE TYR VAL PHE TYR GLU CYS SEQRES 12 A 152 LEU ASP GLY ARG CYS SER GLN PHE SER HET HEM A1001 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *226(H2 O) HELIX 1 1 SER A 6 GLY A 22 1 17 HELIX 2 2 ASP A 23 TYR A 39 1 17 HELIX 3 3 PRO A 40 PHE A 46 5 7 HELIX 4 4 PRO A 53 LYS A 58 1 6 HELIX 5 5 THR A 60 ASN A 80 1 21 HELIX 6 6 ASN A 83 GLY A 96 1 14 HELIX 7 7 PRO A 97 VAL A 99 5 3 HELIX 8 8 THR A 104 HIS A 120 1 17 HELIX 9 9 ASP A 122 ASP A 145 1 24 HELIX 10 10 CYS A 148 SER A 152 5 5 SSBOND 1 CYS A 143 CYS A 148 1555 1555 2.03 LINK NE2 HIS A 98 FE HEM A1001 1555 1555 2.34 LINK FE HEM A1001 O HOH A1002 1555 1555 1.98 SITE 1 AC1 18 LYS A 45 PHE A 46 THR A 48 ARG A 69 SITE 2 AC1 18 ILE A 73 MET A 94 PRO A 97 HIS A 98 SITE 3 AC1 18 ARG A 101 ILE A 103 TYR A 108 PHE A 136 SITE 4 AC1 18 HOH A1002 HOH A1025 HOH A1103 HOH A1153 SITE 5 AC1 18 HOH A1158 HOH A1224 CRYST1 65.144 74.855 33.412 90.00 90.00 90.00 P 21 21 2 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 0.015351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013359 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029930 0.00000