HEADER OXIDOREDUCTASE 03-JUL-20 6ZMU TITLE CRYSTAL STRUCTURE OF THE GERMLINE-SPECIFIC THIOREDOXIN PROTEIN TITLE 2 DEADHEAD (THIOREDOXIN-1) FROM DROSPOHILA MELANOGASTER, P43212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN-1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DMTRX-1,PROTEIN DEADHEAD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: DHD, TRX-1, CG4193; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HOMEOSTASIS, SPERM, OOCYTE-TO-EMBRYO, DNA-BINDING, REDOX, PROTAMINE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.BAGINSKI,R.PLUTA,M.J.MACIAS REVDAT 3 31-JAN-24 6ZMU 1 JRNL REVDAT 2 24-MAR-21 6ZMU 1 JRNL REVDAT 1 21-OCT-20 6ZMU 0 JRNL AUTH R.FREIER,E.ARAGON,B.BAGINSKI,R.PLUTA,P.MARTIN-MALPARTIDA, JRNL AUTH 2 L.RUIZ,M.CONDEMINAS,C.GONZALEZ,M.J.MACIAS JRNL TITL STRUCTURES OF THE GERMLINE-SPECIFIC DEADHEAD AND THIOREDOXIN JRNL TITL 2 T PROTEINS FROM DROSOPHILA MELANOGASTER REVEAL UNIQUE JRNL TITL 3 FEATURES AMONG THIOREDOXINS. JRNL REF IUCRJ V. 8 281 2021 JRNL REFN ESSN 2052-2525 JRNL PMID 33708404 JRNL DOI 10.1107/S2052252521000221 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.FREIER,E.ARAGON,B.BAGINSKI,R.PLUTA,P.MARTIN-MALPARTIDA, REMARK 1 AUTH 2 L.RUIZ,M.CONDEMINAS,C.GONZAEZ,M.MACIAS REMARK 1 TITL STRUCTURES OF THE GERMLINE-SPECIFIC DEADHEAD AND THIOREDOXIN REMARK 1 TITL 2 T PROTEINS FROM DROSOPHILA MELANOGASTER REVEAL UNIQUE REMARK 1 TITL 3 FEATURES AMONG THIOREDOXINS REMARK 1 REF BIORXIV 2020 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2020.07.29.226944 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 41617 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2119 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 436 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 12.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 20 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.40000 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.461 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3554 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3425 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4770 ; 1.753 ; 1.893 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7907 ; 1.173 ; 2.939 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ; 6.500 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;25.705 ;22.549 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 699 ;15.565 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;19.296 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 524 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3763 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 750 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1690 ; 3.866 ; 3.354 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1689 ; 3.862 ; 3.352 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2106 ; 4.856 ; 5.005 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2107 ; 4.856 ; 5.007 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1864 ; 7.660 ; 4.207 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1805 ; 6.663 ; 4.018 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2574 ; 8.739 ; 5.727 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3840 ;10.909 ;39.332 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3828 ;10.889 ;39.237 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 107 REMARK 3 ORIGIN FOR THE GROUP (A): 128.4310 41.3950 109.0370 REMARK 3 T TENSOR REMARK 3 T11: 0.0306 T22: 0.0305 REMARK 3 T33: 0.0465 T12: -0.0091 REMARK 3 T13: 0.0047 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 2.1548 L22: 0.9469 REMARK 3 L33: 3.5199 L12: -0.8665 REMARK 3 L13: -0.9397 L23: 0.0266 REMARK 3 S TENSOR REMARK 3 S11: -0.0223 S12: -0.1927 S13: 0.1643 REMARK 3 S21: -0.0066 S22: 0.1085 S23: 0.0468 REMARK 3 S31: 0.0478 S32: -0.0169 S33: -0.0862 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 105 REMARK 3 ORIGIN FOR THE GROUP (A): 102.5890 48.7370 107.2300 REMARK 3 T TENSOR REMARK 3 T11: 0.1081 T22: 0.2012 REMARK 3 T33: 0.1232 T12: 0.0632 REMARK 3 T13: 0.0428 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 3.4941 L22: 4.3100 REMARK 3 L33: 3.0306 L12: 1.0570 REMARK 3 L13: -0.8730 L23: -1.5702 REMARK 3 S TENSOR REMARK 3 S11: 0.1368 S12: 0.5579 S13: 0.4352 REMARK 3 S21: -0.1373 S22: 0.0104 S23: 0.3706 REMARK 3 S31: -0.3513 S32: -0.2960 S33: -0.1471 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 105 REMARK 3 ORIGIN FOR THE GROUP (A): 111.6690 18.4720 119.9620 REMARK 3 T TENSOR REMARK 3 T11: 0.2003 T22: 0.1963 REMARK 3 T33: 0.3713 T12: 0.0593 REMARK 3 T13: 0.0312 T23: -0.0714 REMARK 3 L TENSOR REMARK 3 L11: 6.4438 L22: 5.8567 REMARK 3 L33: 2.9445 L12: -1.2593 REMARK 3 L13: 1.3370 L23: 0.3291 REMARK 3 S TENSOR REMARK 3 S11: 0.1952 S12: 0.2312 S13: -1.0646 REMARK 3 S21: 0.3447 S22: -0.1335 S23: -0.4058 REMARK 3 S31: 0.6514 S32: 0.3927 S33: -0.0617 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 106 REMARK 3 ORIGIN FOR THE GROUP (A): 83.9230 26.1350 108.7050 REMARK 3 T TENSOR REMARK 3 T11: 0.1180 T22: 0.2648 REMARK 3 T33: 0.0180 T12: -0.0622 REMARK 3 T13: 0.0185 T23: -0.0254 REMARK 3 L TENSOR REMARK 3 L11: 4.3787 L22: 2.8654 REMARK 3 L33: 1.8512 L12: 1.5698 REMARK 3 L13: 0.5583 L23: 0.2595 REMARK 3 S TENSOR REMARK 3 S11: -0.1419 S12: 0.6408 S13: -0.0430 REMARK 3 S21: -0.4781 S22: 0.2330 S23: -0.0793 REMARK 3 S31: 0.1129 S32: -0.2196 S33: -0.0910 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 6ZMU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 77.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 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 FOR SHELL : 1.500 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: 1XWA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.0, 3.2 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 53.49550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.91350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.91350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.24325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.91350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.91350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.74775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.91350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.91350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.24325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.91350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.91350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.74775 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 53.49550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -193.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 GLY B -1 REMARK 465 PRO B 0 REMARK 465 LYS B 106 REMARK 465 ALA B 107 REMARK 465 GLY C -1 REMARK 465 PRO C 0 REMARK 465 LYS C 106 REMARK 465 ALA C 107 REMARK 465 GLY D -1 REMARK 465 PRO D 0 REMARK 465 ALA D 107 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 O1 SO4 A 204 O HOH A 301 1.98 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 GLU B 94 CB GLU B 94 CG 0.118 REMARK 500 GLU B 94 CG GLU B 94 CD 0.099 REMARK 500 ASP C 18 CB ASP C 18 CG 0.132 REMARK 500 GLU C 63 CD GLU C 63 OE1 0.069 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 ASP A 18 CB - CG - OD2 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 81 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 68 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP C 60 CB - CG - OD2 ANGL. DEV. = -5.9 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 ASP A 18 -127.36 53.84 REMARK 500 ASP B 18 -127.12 58.08 REMARK 500 GLN B 82 -119.17 60.11 REMARK 500 ASP C 18 -130.76 59.30 REMARK 500 ASP D 18 -124.06 54.21 REMARK 500 REMARK 500 REMARK: NULL 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 NA B 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 316 O REMARK 620 2 ASP B 60 O 81.7 REMARK 620 3 GLU B 63 OE2 134.9 87.6 REMARK 620 4 ASP C 60 O 90.9 169.4 92.4 REMARK 620 5 GLU C 63 OE2 116.6 100.2 108.4 89.8 REMARK 620 N 1 2 3 4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Z7O RELATED DB: PDB REMARK 900 6Z7O CONTAINS ANOTHER D. MELANOGASTER GERMLINE-SPECIFIC THIOREDOXIN DBREF 6ZMU A 1 107 UNP P47938 THIO1_DROME 1 107 DBREF 6ZMU B 1 107 UNP P47938 THIO1_DROME 1 107 DBREF 6ZMU C 1 107 UNP P47938 THIO1_DROME 1 107 DBREF 6ZMU D 1 107 UNP P47938 THIO1_DROME 1 107 SEQADV 6ZMU GLY A -1 UNP P47938 EXPRESSION TAG SEQADV 6ZMU PRO A 0 UNP P47938 EXPRESSION TAG SEQADV 6ZMU GLY B -1 UNP P47938 EXPRESSION TAG SEQADV 6ZMU PRO B 0 UNP P47938 EXPRESSION TAG SEQADV 6ZMU GLY C -1 UNP P47938 EXPRESSION TAG SEQADV 6ZMU PRO C 0 UNP P47938 EXPRESSION TAG SEQADV 6ZMU GLY D -1 UNP P47938 EXPRESSION TAG SEQADV 6ZMU PRO D 0 UNP P47938 EXPRESSION TAG SEQRES 1 A 109 GLY PRO MET ALA SER VAL ARG THR MET ASN ASP TYR HIS SEQRES 2 A 109 LYS ARG ILE GLU ALA ALA ASP ASP LYS LEU ILE VAL LEU SEQRES 3 A 109 ASP PHE TYR ALA THR TRP CYS GLY PRO CYS LYS GLU MET SEQRES 4 A 109 GLU SER THR VAL LYS SER LEU ALA ARG LYS TYR SER SER SEQRES 5 A 109 LYS ALA VAL VAL LEU LYS ILE ASP VAL ASP LYS PHE GLU SEQRES 6 A 109 GLU LEU THR GLU ARG TYR LYS VAL ARG SER MET PRO THR SEQRES 7 A 109 PHE VAL PHE LEU ARG GLN ASN ARG ARG LEU ALA SER PHE SEQRES 8 A 109 ALA GLY ALA ASP GLU HIS LYS LEU THR ASN MET MET ALA SEQRES 9 A 109 LYS LEU VAL LYS ALA SEQRES 1 B 109 GLY PRO MET ALA SER VAL ARG THR MET ASN ASP TYR HIS SEQRES 2 B 109 LYS ARG ILE GLU ALA ALA ASP ASP LYS LEU ILE VAL LEU SEQRES 3 B 109 ASP PHE TYR ALA THR TRP CYS GLY PRO CYS LYS GLU MET SEQRES 4 B 109 GLU SER THR VAL LYS SER LEU ALA ARG LYS TYR SER SER SEQRES 5 B 109 LYS ALA VAL VAL LEU LYS ILE ASP VAL ASP LYS PHE GLU SEQRES 6 B 109 GLU LEU THR GLU ARG TYR LYS VAL ARG SER MET PRO THR SEQRES 7 B 109 PHE VAL PHE LEU ARG GLN ASN ARG ARG LEU ALA SER PHE SEQRES 8 B 109 ALA GLY ALA ASP GLU HIS LYS LEU THR ASN MET MET ALA SEQRES 9 B 109 LYS LEU VAL LYS ALA SEQRES 1 C 109 GLY PRO MET ALA SER VAL ARG THR MET ASN ASP TYR HIS SEQRES 2 C 109 LYS ARG ILE GLU ALA ALA ASP ASP LYS LEU ILE VAL LEU SEQRES 3 C 109 ASP PHE TYR ALA THR TRP CYS GLY PRO CYS LYS GLU MET SEQRES 4 C 109 GLU SER THR VAL LYS SER LEU ALA ARG LYS TYR SER SER SEQRES 5 C 109 LYS ALA VAL VAL LEU LYS ILE ASP VAL ASP LYS PHE GLU SEQRES 6 C 109 GLU LEU THR GLU ARG TYR LYS VAL ARG SER MET PRO THR SEQRES 7 C 109 PHE VAL PHE LEU ARG GLN ASN ARG ARG LEU ALA SER PHE SEQRES 8 C 109 ALA GLY ALA ASP GLU HIS LYS LEU THR ASN MET MET ALA SEQRES 9 C 109 LYS LEU VAL LYS ALA SEQRES 1 D 109 GLY PRO MET ALA SER VAL ARG THR MET ASN ASP TYR HIS SEQRES 2 D 109 LYS ARG ILE GLU ALA ALA ASP ASP LYS LEU ILE VAL LEU SEQRES 3 D 109 ASP PHE TYR ALA THR TRP CYS GLY PRO CYS LYS GLU MET SEQRES 4 D 109 GLU SER THR VAL LYS SER LEU ALA ARG LYS TYR SER SER SEQRES 5 D 109 LYS ALA VAL VAL LEU LYS ILE ASP VAL ASP LYS PHE GLU SEQRES 6 D 109 GLU LEU THR GLU ARG TYR LYS VAL ARG SER MET PRO THR SEQRES 7 D 109 PHE VAL PHE LEU ARG GLN ASN ARG ARG LEU ALA SER PHE SEQRES 8 D 109 ALA GLY ALA ASP GLU HIS LYS LEU THR ASN MET MET ALA SEQRES 9 D 109 LYS LEU VAL LYS ALA HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HET SO4 A 206 5 HET SO4 B 201 5 HET SO4 B 202 5 HET SO4 B 203 5 HET SO4 B 204 5 HET NA B 205 1 HET SO4 D 201 5 HET SO4 D 202 5 HET SO4 D 203 5 HET SO4 D 204 5 HET SO4 D 205 5 HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION FORMUL 5 SO4 15(O4 S 2-) FORMUL 15 NA NA 1+ FORMUL 21 HOH *94(H2 O) HELIX 1 AA1 THR A 6 ALA A 17 1 12 HELIX 2 AA2 CYS A 31 TYR A 48 1 18 HELIX 3 AA3 PHE A 62 TYR A 69 1 8 HELIX 4 AA4 ASP A 93 VAL A 105 1 13 HELIX 5 AA5 THR B 6 ALA B 16 1 11 HELIX 6 AA6 CYS B 31 TYR B 48 1 18 HELIX 7 AA7 PHE B 62 TYR B 69 1 8 HELIX 8 AA8 ASP B 93 VAL B 105 1 13 HELIX 9 AA9 THR C 6 ALA C 17 1 12 HELIX 10 AB1 CYS C 31 TYR C 48 1 18 HELIX 11 AB2 PHE C 62 TYR C 69 1 8 HELIX 12 AB3 ASP C 93 VAL C 105 1 13 HELIX 13 AB4 THR D 6 ALA D 17 1 12 HELIX 14 AB5 CYS D 31 TYR D 48 1 18 HELIX 15 AB6 PHE D 62 TYR D 69 1 8 HELIX 16 AB7 ASP D 93 VAL D 105 1 13 SHEET 1 AA1 5 ALA A 2 SER A 3 0 SHEET 2 AA1 5 ALA A 52 ASP A 58 1 O LYS A 56 N ALA A 2 SHEET 3 AA1 5 LEU A 21 TYR A 27 1 N ASP A 25 O LEU A 55 SHEET 4 AA1 5 THR A 76 ARG A 81 -1 O VAL A 78 N LEU A 24 SHEET 5 AA1 5 ARG A 84 ALA A 90 -1 O LEU A 86 N PHE A 79 SHEET 1 AA2 5 ALA B 2 SER B 3 0 SHEET 2 AA2 5 ALA B 52 ASP B 58 1 O LYS B 56 N ALA B 2 SHEET 3 AA2 5 LEU B 21 TYR B 27 1 N ASP B 25 O LEU B 55 SHEET 4 AA2 5 THR B 76 ARG B 81 -1 O LEU B 80 N ILE B 22 SHEET 5 AA2 5 ARG B 84 ALA B 90 -1 O LEU B 86 N PHE B 79 SHEET 1 AA3 5 ALA C 2 SER C 3 0 SHEET 2 AA3 5 ALA C 52 ASP C 58 1 O LYS C 56 N ALA C 2 SHEET 3 AA3 5 LEU C 21 TYR C 27 1 N VAL C 23 O LEU C 55 SHEET 4 AA3 5 THR C 76 ARG C 81 -1 O LEU C 80 N ILE C 22 SHEET 5 AA3 5 ARG C 84 ALA C 90 -1 O LEU C 86 N PHE C 79 SHEET 1 AA4 5 ALA D 2 SER D 3 0 SHEET 2 AA4 5 ALA D 52 ASP D 58 1 O LYS D 56 N ALA D 2 SHEET 3 AA4 5 LEU D 21 TYR D 27 1 N VAL D 23 O LEU D 55 SHEET 4 AA4 5 THR D 76 ARG D 81 -1 O LEU D 80 N ILE D 22 SHEET 5 AA4 5 ARG D 84 ALA D 90 -1 O LEU D 86 N PHE D 79 LINK ND2 ASN A 8 O4 SO4 A 202 1555 1555 1.44 LINK O HOH A 316 NA NA B 205 4565 1555 2.36 LINK O ASP B 60 NA NA B 205 1555 1555 2.28 LINK OE2 GLU B 63 NA NA B 205 1555 1555 2.34 LINK NA NA B 205 O ASP C 60 1555 1555 2.22 LINK NA NA B 205 OE2 GLU C 63 1555 1555 2.21 CISPEP 1 MET A 74 PRO A 75 0 -6.81 CISPEP 2 MET B 74 PRO B 75 0 -7.37 CISPEP 3 MET C 74 PRO C 75 0 -4.92 CISPEP 4 MET D 74 PRO D 75 0 -7.58 SITE 1 AC1 4 HOH A 313 HOH C 202 ARG D 81 ARG D 84 SITE 1 AC2 3 THR A 6 ASN A 8 LYS A 12 SITE 1 AC3 4 TYR A 10 HIS A 11 ARG A 68 TYR A 69 SITE 1 AC4 4 ALA A 87 SER A 88 HOH A 301 ARG B 68 SITE 1 AC5 1 ARG A 13 SITE 1 AC6 3 MET A 1 ALA A 2 SER A 3 SITE 1 AC7 8 PHE A 89 LYS A 96 MET B 7 TYR B 10 SITE 2 AC7 8 HIS B 11 LEU B 65 ARG B 68 HOH B 303 SITE 1 AC8 3 LYS B 70 ARG B 72 ARG B 84 SITE 1 AC9 5 HIS A 95 ARG B 85 LEU B 86 ALA B 87 SITE 2 AC9 5 SER B 88 SITE 1 AD1 5 GLY A 32 LYS A 103 LYS B 70 ARG B 72 SITE 2 AD1 5 HOH B 301 SITE 1 AD2 5 HOH A 316 ASP B 60 GLU B 63 ASP C 60 SITE 2 AD2 5 GLU C 63 SITE 1 AD3 2 PHE D 89 ALA D 90 SITE 1 AD4 5 MET D 7 HIS D 11 GLU D 64 ARG D 68 SITE 2 AD4 5 SO4 D 203 SITE 1 AD5 7 ASP A 19 GLN A 82 TYR D 10 HIS D 11 SITE 2 AD5 7 ARG D 68 TYR D 69 SO4 D 202 SITE 1 AD6 1 ARG D 13 SITE 1 AD7 5 LYS B 35 ARG D 5 THR D 6 ASN D 8 SITE 2 AD7 5 ASP D 9 CRYST1 111.827 111.827 106.991 90.00 90.00 90.00 P 43 21 2 32 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 0.008942 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009347 0.00000