HEADER OXIDOREDUCTASE 19-JUN-13 3WDN TITLE HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURE OF BOVINE H-PROTEIN USING A TITLE 2 HIGH-PRESSURE CRYOCOOLING METHOD COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: GCSH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS ANTIPARALLEL BETA SHEET, BETA SANDWICH, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.HIGASHIURA,A.NAKAGAWA REVDAT 3 08-NOV-23 3WDN 1 REMARK REVDAT 2 11-DEC-13 3WDN 1 HEADER REVDAT 1 30-OCT-13 3WDN 0 JRNL AUTH A.HIGASHIURA,K.OHTA,M.MASAKI,M.SATO,K.INAKA,H.TANAKA, JRNL AUTH 2 A.NAKAGAWA JRNL TITL HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURE OF BOVINE H-PROTEIN JRNL TITL 2 USING THE HIGH-PRESSURE CRYOCOOLING METHOD JRNL REF J.SYNCHROTRON RADIAT. V. 20 989 2013 JRNL REFN ISSN 0909-0495 JRNL PMID 24121354 JRNL DOI 10.1107/S090904951302373X REMARK 2 REMARK 2 RESOLUTION. 0.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.114 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 126382 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)) : NULL 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 973 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 2.206 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000096203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 3.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126382 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.860 REMARK 200 RESOLUTION RANGE LOW (A) : 30.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.850 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3KLR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6-1.6M AMMONIUM SULPHATE, 0-30% REMARK 280 GLYCEROL, 0.1M SODIUM CITRATE, PH 3.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 42.43500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.70750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.43500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.70750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 NZ LYS A 4 O HOH A 554 0.98 REMARK 500 OE2 GLU A 63 O HOH A 544 1.09 REMARK 500 CE LYS A 59 O HOH A 573 1.54 REMARK 500 NZ LYS A 59 O HOH A 573 1.57 REMARK 500 NZ LYS A 59 O HOH A 573 1.60 REMARK 500 NZ LYS A 59 O HOH A 555 1.65 REMARK 500 ND2 ASN A 82 O HOH A 532 1.80 REMARK 500 CE LYS A 59 O HOH A 573 1.87 REMARK 500 OD1 ASN A 82 O HOH A 484 1.88 REMARK 500 OD1 ASP A 33 O HOH A 323 1.93 REMARK 500 OD1 ASP A 33 O HOH A 365 2.04 REMARK 500 CD GLU A 63 O HOH A 544 2.10 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 3 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG A 3 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 3 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLU A 15 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 LEU A 107 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 ASP A 108 CA - C - N ANGL. DEV. = -14.8 DEGREES REMARK 500 ASP A 108 O - C - N ANGL. DEV. = 14.1 DEGREES REMARK 500 GLU A 109 OE1 - CD - OE2 ANGL. DEV. = -12.2 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 HIS A 9 30.07 73.56 REMARK 500 ASN A 16 52.10 38.67 REMARK 500 GLN A 49 -10.62 86.65 REMARK 500 GLN A 49 -0.30 79.29 REMARK 500 SER A 89 58.37 -150.44 REMARK 500 GLU A 92 -91.75 -129.62 REMARK 500 GLU A 92 -91.70 -129.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 DBREF 3WDN A 1 125 UNP P20821 GCSH_BOVIN 49 173 SEQRES 1 A 125 SER VAL ARG LYS PHE THR GLU LYS HIS GLU TRP VAL THR SEQRES 2 A 125 THR GLU ASN GLY VAL GLY THR VAL GLY ILE SER ASN PHE SEQRES 3 A 125 ALA GLN GLU ALA LEU GLY ASP VAL VAL TYR CYS SER LEU SEQRES 4 A 125 PRO GLU VAL GLY THR LYS LEU ASN LYS GLN GLU GLU PHE SEQRES 5 A 125 GLY ALA LEU GLU SER VAL LYS ALA ALA SER GLU LEU TYR SEQRES 6 A 125 SER PRO LEU SER GLY GLU VAL THR GLU ILE ASN LYS ALA SEQRES 7 A 125 LEU ALA GLU ASN PRO GLY LEU VAL ASN LYS SER CYS TYR SEQRES 8 A 125 GLU ASP GLY TRP LEU ILE LYS MET THR PHE SER ASN PRO SEQRES 9 A 125 SER GLU LEU ASP GLU LEU MET SER GLU GLU ALA TYR GLU SEQRES 10 A 125 LYS TYR ILE LYS SER ILE GLU GLU HET GOL A 201 12 HET GOL A 202 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *292(H2 O) HELIX 1 1 SER A 24 GLY A 32 1 9 HELIX 2 2 LYS A 77 ALA A 80 5 4 HELIX 3 3 GLY A 84 SER A 89 1 6 HELIX 4 4 ASN A 103 LEU A 110 5 8 HELIX 5 5 GLU A 113 GLU A 125 1 13 SHEET 1 A 7 LYS A 45 LEU A 46 0 SHEET 2 A 7 GLY A 70 ILE A 75 -1 O GLY A 70 N LEU A 46 SHEET 3 A 7 ILE A 97 PHE A 101 -1 O LYS A 98 N THR A 73 SHEET 4 A 7 VAL A 18 ILE A 23 -1 N GLY A 19 O MET A 99 SHEET 5 A 7 GLU A 10 GLU A 15 -1 N THR A 13 O THR A 20 SHEET 6 A 7 LYS A 4 PHE A 5 -1 N LYS A 4 O VAL A 12 SHEET 7 A 7 MET A 111 SER A 112 -1 O MET A 111 N PHE A 5 SHEET 1 B 3 VAL A 34 SER A 38 0 SHEET 2 B 3 GLU A 51 SER A 57 -1 O ALA A 54 N SER A 38 SHEET 3 B 3 ALA A 61 TYR A 65 -1 O LEU A 64 N GLY A 53 SITE 1 AC1 12 ASN A 25 LYS A 59 ALA A 60 ASN A 87 SITE 2 AC1 12 LYS A 88 SER A 89 CYS A 90 HOH A 316 SITE 3 AC1 12 HOH A 328 HOH A 432 HOH A 466 HOH A 467 SITE 1 AC2 7 ARG A 3 LYS A 59 GLU A 113 HOH A 413 SITE 2 AC2 7 HOH A 424 HOH A 505 HOH A 575 CRYST1 84.870 41.415 43.317 90.00 91.72 90.00 C 1 2 1 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 0.011783 0.000000 0.000354 0.00000 SCALE2 0.000000 0.024146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023096 0.00000