HEADER RIBOSOMAL PROTEIN 27-SEP-17 5YH1 TITLE MEMBER OF S1P FAMILY OF RIBOSOMAL PROTEINS PF0399 DHH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBER OF S1P FAMILY OF RIBOSOMAL PROTEINS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DHH DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS (STRAIN ATCC 43587 / DSM SOURCE 3 3638 / JCM 8422 / VC1); SOURCE 4 ORGANISM_TAXID: 186497; SOURCE 5 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 6 GENE: PF0399; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PF0399, DHH DOMAIN, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.SONG,X.P.LIU REVDAT 1 01-AUG-18 5YH1 0 JRNL AUTH Y.SONG,X.P.LIU JRNL TITL MEMBER OF S1P FAMILY OF RIBOSOMAL PROTEINS PF0399 DHH DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 48383 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) : 0.187 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2583 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) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2180 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.02000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3607 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3501 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4869 ; 1.130 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8086 ; 0.732 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 438 ; 5.060 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;32.762 ;23.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 609 ;13.856 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.225 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3984 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 780 ; 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): 1755 ; 1.381 ; 3.281 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1754 ; 1.381 ; 3.281 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2192 ; 2.237 ; 4.916 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2193 ; 2.237 ; 4.916 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1852 ; 2.178 ; 3.616 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1852 ; 2.177 ; 3.616 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2678 ; 3.498 ; 5.283 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4145 ; 5.176 ;26.498 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4145 ; 5.175 ;26.498 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-15 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 : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56239 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 33.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% (V/V) PEG 400 100 MM SODIUM REMARK 280 ACETATE/ ACETIC ACID PH 5.5 2000 MM LITHIUM SULFATE 100 MM REMARK 280 MAGNESIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.12250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 106.12250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 106.12250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 106.12250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 106.12250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 106.12250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 132.50000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 66.25000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 114.74837 REMARK 350 BIOMT3 3 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 739 REMARK 465 GLU A 740 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MSE A 304 CG SE CE REMARK 470 ARG A 402 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 466 CZ NH1 NH2 REMARK 470 LYS A 605 CE NZ REMARK 470 LYS A 693 CD CE NZ REMARK 470 LYS A 716 CD CE NZ REMARK 470 LYS A 731 CG CD CE NZ 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 SER A 330 117.98 -169.33 REMARK 500 ALA A 363 49.32 -91.99 REMARK 500 ARG A 466 -61.49 70.37 REMARK 500 LYS A 567 -107.77 56.71 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 MN A 805 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 366 OD2 REMARK 620 2 ASP A 436 OD1 87.9 REMARK 620 3 HIS A 462 NE2 89.2 78.6 REMARK 620 4 ASP A 528 OD2 83.6 165.2 89.2 REMARK 620 5 HOH A 909 O 103.4 95.4 165.9 98.3 REMARK 620 6 HOH A 929 O 167.2 104.3 89.3 83.6 79.8 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 GOL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 805 DBREF 5YH1 A 305 740 UNP Q8U3Q7 Q8U3Q7_PYRFU 305 740 SEQADV 5YH1 PRO A 300 UNP Q8U3Q7 EXPRESSION TAG SEQADV 5YH1 GLY A 301 UNP Q8U3Q7 EXPRESSION TAG SEQADV 5YH1 SER A 302 UNP Q8U3Q7 EXPRESSION TAG SEQADV 5YH1 HIS A 303 UNP Q8U3Q7 EXPRESSION TAG SEQADV 5YH1 MSE A 304 UNP Q8U3Q7 EXPRESSION TAG SEQRES 1 A 441 PRO GLY SER HIS MSE ALA GLU VAL LYS ARG LYS ILE GLU SEQRES 2 A 441 GLU GLU LEU ASP ARG ARG ALA GLN PRO SER ASP VAL GLY SEQRES 3 A 441 PHE LEU VAL LYS SER GLU VAL LEU GLU ALA LEU LYS PRO SEQRES 4 A 441 LYS ILE MSE LYS ALA ALA PHE MSE ILE ARG ARG ALA ILE SEQRES 5 A 441 PHE GLU GLY ARG PRO ILE ILE LEU ARG HIS HIS ALA ASP SEQRES 6 A 441 THR ASP GLY TYR THR ALA GLY VAL ALA LEU GLU THR ALA SEQRES 7 A 441 ILE ILE PRO LEU ILE GLU LYS VAL ALA PRO ASP PRO GLU SEQRES 8 A 441 ALA ARG TRP HIS LEU PHE LYS ARG ARG PRO SER ARG ALA SEQRES 9 A 441 PRO PHE TYR GLU LEU GLU ASP VAL LEU LYS ASP ILE ILE SEQRES 10 A 441 PHE MSE MSE GLU ASP HIS MSE ARG PHE GLY ASP GLU LEU SEQRES 11 A 441 PRO LEU VAL VAL ILE VAL ASP ASN GLY GLY THR THR GLU SEQRES 12 A 441 ASP ILE PRO ALA TYR LYS ARG LEU LYS ALA TYR GLY VAL SEQRES 13 A 441 LYS ILE VAL VAL ILE ASP HIS HIS ASP PRO ARG ASP TRP SEQRES 14 A 441 ILE SER GLU ASP LYS ALA LYS VAL ASP GLU TYR VAL ASP SEQRES 15 A 441 VAL HIS VAL ASN PRO HIS HIS VAL LYS ARG GLY TYR TYR SEQRES 16 A 441 GLU LEU THR ALA GLY MSE LEU ALA THR GLU VAL ALA ARG SEQRES 17 A 441 TYR ILE ASN PRO GLU VAL GLU ASP ARG ILE LYS HIS LEU SEQRES 18 A 441 PRO ALA ILE ALA GLY THR GLY ASP ARG SER LYS ALA PRO SEQRES 19 A 441 GLU PHE TYR GLN TYR LEU GLU TYR ALA LYS GLU LYS GLY SEQRES 20 A 441 LEU ASP GLU GLU ASP LEU LYS LYS ILE ALA GLU VAL ILE SEQRES 21 A 441 ASP HIS GLU ALA PHE TYR TRP LYS PHE MSE ASP GLY ARG SEQRES 22 A 441 GLY ILE ILE GLU GLU ILE LEU LEU ILE THR GLY ASN LEU SEQRES 23 A 441 GLN ARG HIS ARG MSE LEU VAL GLU GLY ILE TYR PRO GLU SEQRES 24 A 441 VAL LYS GLU LYS GLN GLU LYS VAL LEU LYS ALA VAL LEU SEQRES 25 A 441 PRO HIS VAL LYS SER VAL VAL LEU PRO ASN GLY ILE ARG SEQRES 26 A 441 PHE ASN THR ILE ASP VAL GLU LEU TYR ALA PRO LYS PHE SEQRES 27 A 441 GLU TYR PRO SER PRO GLY LYS LEU SER GLY ILE ILE HIS SEQRES 28 A 441 ASP HIS PHE LYS GLU GLN TYR GLY GLU ASP SER PRO ILE SEQRES 29 A 441 LEU THR LEU ALA TYR GLY PRO ASP PHE ALA VAL VAL ARG SEQRES 30 A 441 ALA SER ASP GLY MSE ALA LYS TYR ASN PHE ASP LEU ASN SEQRES 31 A 441 LYS ILE VAL LYS ILE LEU ALA GLU LYS LEU PRO ASP ALA SEQRES 32 A 441 GLY VAL GLU GLY GLY GLY HIS SER TYR ALA GLY SER ILE SEQRES 33 A 441 LYS PHE PHE GLU GLY LYS ARG LYS GLU VAL LEU GLU ALA SEQRES 34 A 441 PHE ALA LYS GLU VAL LEU LYS LEU LYS ALA GLY GLU MODRES 5YH1 MSE A 341 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 346 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 418 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 419 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 423 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 500 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 569 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 590 MET MODIFIED RESIDUE MODRES 5YH1 MSE A 681 MET MODIFIED RESIDUE HET MSE A 304 5 HET MSE A 341 8 HET MSE A 346 8 HET MSE A 418 8 HET MSE A 419 8 HET MSE A 423 8 HET MSE A 500 8 HET MSE A 569 8 HET MSE A 590 8 HET MSE A 681 8 HET GOL A 801 6 HET GOL A 802 6 HET GOL A 803 6 HET GOL A 804 6 HET MN A 805 1 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETNAM MN MANGANESE (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 MN MN 2+ FORMUL 7 HOH *159(H2 O) HELIX 1 AA1 PRO A 300 GLN A 320 1 21 HELIX 2 AA2 SER A 330 GLU A 353 1 24 HELIX 3 AA3 ASP A 364 ALA A 386 1 23 HELIX 4 AA4 GLU A 390 LEU A 395 1 6 HELIX 5 AA5 GLU A 407 GLY A 426 1 20 HELIX 6 AA6 THR A 440 GLU A 442 5 3 HELIX 7 AA7 ASP A 443 ALA A 452 1 10 HELIX 8 AA8 VAL A 476 VAL A 480 5 5 HELIX 9 AA9 ASN A 485 VAL A 489 5 5 HELIX 10 AB1 THR A 497 ASN A 510 1 14 HELIX 11 AB2 VAL A 513 LYS A 518 1 6 HELIX 12 AB3 HIS A 519 ARG A 529 1 11 HELIX 13 AB4 ALA A 532 LYS A 545 1 14 HELIX 14 AB5 ASP A 548 LYS A 567 1 20 HELIX 15 AB6 ILE A 574 LEU A 579 1 6 HELIX 16 AB7 ASN A 584 LEU A 611 1 28 HELIX 17 AB8 PRO A 612 VAL A 614 5 3 HELIX 18 AB9 SER A 641 GLY A 658 1 18 HELIX 19 AC1 ASP A 679 ASN A 685 5 7 HELIX 20 AC2 ASP A 687 LEU A 699 1 13 HELIX 21 AC3 PRO A 700 GLY A 703 5 4 HELIX 22 AC4 PHE A 718 GLY A 720 5 3 HELIX 23 AC5 LYS A 721 LYS A 735 1 15 SHEET 1 AA1 5 PHE A 396 SER A 401 0 SHEET 2 AA1 5 ILE A 357 HIS A 362 1 N LEU A 359 O LYS A 397 SHEET 3 AA1 5 LEU A 431 VAL A 435 1 O VAL A 433 N ILE A 358 SHEET 4 AA1 5 ILE A 457 ILE A 460 1 O VAL A 458 N VAL A 432 SHEET 5 AA1 5 VAL A 482 VAL A 484 1 O VAL A 484 N VAL A 459 SHEET 1 AA2 2 TRP A 468 SER A 470 0 SHEET 2 AA2 2 LYS A 473 ALA A 474 -1 O LYS A 473 N ILE A 469 SHEET 1 AA3 6 LYS A 615 VAL A 618 0 SHEET 2 AA3 6 ARG A 624 ASP A 629 -1 O PHE A 625 N VAL A 617 SHEET 3 AA3 6 ILE A 663 TYR A 668 1 O LEU A 666 N ASN A 626 SHEET 4 AA3 6 PHE A 672 ALA A 677 -1 O VAL A 674 N ALA A 667 SHEET 5 AA3 6 ALA A 712 LYS A 716 -1 O GLY A 713 N VAL A 675 SHEET 6 AA3 6 GLU A 705 GLY A 708 -1 N GLU A 705 O LYS A 716 LINK C HIS A 303 N MSE A 304 1555 1555 1.33 LINK C MSE A 304 N ALA A 305 1555 1555 1.33 LINK C ILE A 340 N MSE A 341 1555 1555 1.33 LINK C MSE A 341 N LYS A 342 1555 1555 1.32 LINK C PHE A 345 N MSE A 346 1555 1555 1.33 LINK C MSE A 346 N ILE A 347 1555 1555 1.33 LINK OD2 ASP A 366 MN MN A 805 1555 1555 2.11 LINK C PHE A 417 N MSE A 418 1555 1555 1.33 LINK C MSE A 418 N MSE A 419 1555 1555 1.33 LINK C MSE A 419 N GLU A 420 1555 1555 1.33 LINK C HIS A 422 N MSE A 423 1555 1555 1.33 LINK C MSE A 423 N ARG A 424 1555 1555 1.32 LINK OD1 ASP A 436 MN MN A 805 1555 1555 2.31 LINK NE2 HIS A 462 MN MN A 805 1555 1555 2.39 LINK C GLY A 499 N MSE A 500 1555 1555 1.33 LINK C MSE A 500 N LEU A 501 1555 1555 1.32 LINK OD2 ASP A 528 MN MN A 805 1555 1555 2.23 LINK C PHE A 568 N MSE A 569 1555 1555 1.33 LINK C MSE A 569 N ASP A 570 1555 1555 1.33 LINK C ARG A 589 N MSE A 590 1555 1555 1.32 LINK C MSE A 590 N LEU A 591 1555 1555 1.33 LINK C GLY A 680 N MSE A 681 1555 1555 1.34 LINK C MSE A 681 N ALA A 682 1555 1555 1.33 LINK MN MN A 805 O HOH A 909 1555 1555 2.17 LINK MN MN A 805 O HOH A 929 1555 1555 2.23 CISPEP 1 TYR A 639 PRO A 640 0 1.57 SITE 1 AC1 2 SER A 322 ASP A 323 SITE 1 AC2 3 ARG A 355 GLU A 428 LEU A 429 SITE 1 AC3 2 HIS A 422 ARG A 587 SITE 1 AC4 6 LEU A 408 PRO A 445 GLU A 598 LYS A 602 SITE 2 AC4 6 HOH A 933 HOH A 982 SITE 1 AC5 6 ASP A 366 ASP A 436 HIS A 462 ASP A 528 SITE 2 AC5 6 HOH A 909 HOH A 929 CRYST1 132.500 132.500 212.245 90.00 90.00 120.00 P 63 2 2 12 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 0.007547 0.004357 0.000000 0.00000 SCALE2 0.000000 0.008715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004712 0.00000