HEADER OXIDOREDUCTASE 06-APR-20 6YKB TITLE [FE]-HYDROGENASE FROM METHANOLACINIA PAYNTERI IN COMPLEX WITH GMP AT TITLE 2 1.55-A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN [FE]-HYDROGENASE; COMPND 3 CHAIN: A, C; COMPND 4 EC: 1.12.98.2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE HIS-TAG IS LOCATED IN THE C-TERMINAL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOLACINIA PAYNTERI G-2000; SOURCE 3 ORGANISM_TAXID: 694436; SOURCE 4 VARIANT: DSM 2545; SOURCE 5 CELL_LINE: /; SOURCE 6 ATCC: /; SOURCE 7 ORGAN: /; SOURCE 8 TISSUE: /; SOURCE 9 CELL: /; SOURCE 10 GENE: HMD; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_ATCC_NUMBER: /; SOURCE 14 EXPRESSION_SYSTEM_ORGAN: /; SOURCE 15 EXPRESSION_SYSTEM_TISSUE: /; SOURCE 16 EXPRESSION_SYSTEM_CELL: /; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET-24B(+) KEYWDS [FE]-HYDROGENASE; FEGP COFACTOR; GUANYLYLPYRIDINOL; CONFORMATIONAL KEYWDS 2 CHANGES; GMP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WAGNER,G.HUANG,F.J.ARRIAZA-GALLARDO,S.SHIMA REVDAT 2 24-JAN-24 6YKB 1 REMARK REVDAT 1 17-FEB-21 6YKB 0 JRNL AUTH G.HUANG,T.WAGNER,U.DEMMER,E.WARKENTIN,U.ERMLER,S.SHIMA JRNL TITL THE HYDRIDE TRANSFER PROCESS IN NADP-DEPENDENT JRNL TITL 2 METHYLENE-TETRAHYDROMETHANOPTERIN DEHYDROGENASE. JRNL REF J.MOL.BIOL. V. 432 2042 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32061937 JRNL DOI 10.1016/J.JMB.2020.01.042 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 104777 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 5065 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 7722 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2135 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7372 REMARK 3 BIN R VALUE (WORKING SET) : 0.2119 REMARK 3 BIN FREE R VALUE : 0.2464 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.53 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 350 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5197 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.46570 REMARK 3 B22 (A**2) : 2.26870 REMARK 3 B33 (A**2) : -4.73440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.44520 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.220 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.081 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.079 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.091 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.077 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 10876 ; 4.000 ; HARMONIC REMARK 3 BOND ANGLES : 19813 ; 4.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2442 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1684 ; 20.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 10876 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 760 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 12292 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.08 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.27 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 83.0443 -10.6121 41.2078 REMARK 3 T TENSOR REMARK 3 T11: -0.0735 T22: -0.0355 REMARK 3 T33: -0.0204 T12: 0.0103 REMARK 3 T13: 0.0038 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6189 L22: 0.5363 REMARK 3 L33: 1.1927 L12: 0.1524 REMARK 3 L13: -0.3723 L23: -0.4388 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: -0.1233 S13: -0.0760 REMARK 3 S21: -0.0169 S22: -0.0878 S23: -0.0531 REMARK 3 S31: 0.0273 S32: 0.2484 S33: 0.0872 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 83.7656 11.9304 7.4172 REMARK 3 T TENSOR REMARK 3 T11: -0.0125 T22: -0.0670 REMARK 3 T33: -0.0372 T12: 0.0149 REMARK 3 T13: 0.0245 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.4441 L22: 0.8546 REMARK 3 L33: 0.7638 L12: -0.1753 REMARK 3 L13: 0.1756 L23: -0.5471 REMARK 3 S TENSOR REMARK 3 S11: 0.0527 S12: 0.0530 S13: 0.0860 REMARK 3 S21: -0.1483 S22: -0.1217 S23: -0.0894 REMARK 3 S31: 0.0821 S32: 0.1503 S33: 0.0690 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YKB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292106729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 104812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 95.095 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35300 REMARK 200 R SYM FOR SHELL (I) : 0.35300 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4JJF REMARK 200 REMARK 200 REMARK: LARGE ROD SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FE-HYDROGENASE HOLOENZYME FROM REMARK 280 METHANOLACINIA PAYNTERI WAS CRYSTALLIZED UNDER 95%N2/5%H2 AT 8 REMARK 280 DEGREE CELSIUS USING A 96-WELL TWO-DROP MRC CRYSTALLIZATION REMARK 280 PLATES. 0.7 UL OF 25 MG/ML RECONSTITUTED ENZYME WITH AN FE(II)- REMARK 280 COMPLEX MIMICKING THE FEGP COFACTOR AND GMP (2MM FINAL) WAS REMARK 280 MIXED WITH 0.7-UL RESERVOIR SOLUTION UNDER YELLOW LIGHT AND REMARK 280 INCUBATED UNDER DARK CONDITIONS. THE BEST CRYSTAL APPEARED REMARK 280 WITHIN ONE MONTH IN 20% W/V POLYETHYLENE GLYCOL 3350 AND 200-MM REMARK 280 MAGNESIUM FORMATE RESERVOIR SOLUTION (JBSCREEN WIZARD 3&4 HTS, REMARK 280 JENA BIOSCIENCE). THE CRYO PROTECTION WAS PERFORMED BY ADDING 30% REMARK 280 GLYCEROL FINAL TO THE CRYSTALLIZATION SOLUTION., PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 283.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.52900 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 1 REMARK 465 MET C 1 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 45 -137.78 51.87 REMARK 500 GLU A 90 -115.06 -119.63 REMARK 500 GLU A 93 0.37 -69.23 REMARK 500 LYS A 150 91.96 -69.49 REMARK 500 THR A 176 24.29 45.54 REMARK 500 THR A 198 -157.53 -151.15 REMARK 500 ALA A 204 168.60 179.41 REMARK 500 SER C 45 -137.27 52.13 REMARK 500 GLU C 90 -102.16 -122.64 REMARK 500 LYS C 150 89.77 -68.56 REMARK 500 THR C 176 24.46 45.72 REMARK 500 THR C 198 -157.96 -151.26 REMARK 500 ALA C 204 175.36 174.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 816 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 817 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 818 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 819 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A 820 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH C 817 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH C 818 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH C 819 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH C 820 DISTANCE = 6.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT C 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT C 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT C 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 405 DBREF 6YKB A 1 342 PDB 6YKB 6YKB 1 342 DBREF 6YKB C 1 342 PDB 6YKB 6YKB 1 342 SEQRES 1 A 342 MET THR ILE LYS LYS VAL ALA ILE LEU GLY ALA GLY CYS SEQRES 2 A 342 TYR ARG THR HIS SER ALA THR GLY ILE THR ASN PHE ALA SEQRES 3 A 342 ARG ALA CYS GLU VAL ALA GLU MET VAL GLY LYS PRO GLU SEQRES 4 A 342 ILE ALA MET THR HIS SER THR ILE ALA MET ALA ALA GLU SEQRES 5 A 342 LEU LYS TYR LEU ALA GLY ILE ASP ASN ILE VAL ILE SER SEQRES 6 A 342 ASP PRO SER PHE ALA GLY GLU PHE THR VAL VAL LYS ASP SEQRES 7 A 342 PHE ASP TYR ASN GLU VAL ILE LYS ALA HIS LYS GLU ASN SEQRES 8 A 342 PRO GLU THR ILE MET PRO LYS ILE ARG GLU LYS VAL ASN SEQRES 9 A 342 GLU LEU ALA LYS THR VAL PRO LYS PRO PRO LYS GLY ALA SEQRES 10 A 342 ILE HIS PHE VAL HIS PRO GLU ASP LEU GLY LEU LYS VAL SEQRES 11 A 342 THR THR ASP ASP ARG GLU ALA VAL ARG ASP ALA ASP LEU SEQRES 12 A 342 ILE ILE THR TRP LEU PRO LYS GLY ASP MET GLN LYS GLY SEQRES 13 A 342 ILE ILE GLU LYS PHE ALA GLY ASP ILE LYS GLN GLY ALA SEQRES 14 A 342 ILE ILE THR HIS ALA CYS THR ILE PRO THR THR LEU PHE SEQRES 15 A 342 TYR LYS ILE PHE GLU GLU LEU GLY ILE ALA ASP LYS VAL SEQRES 16 A 342 GLU VAL THR SER TYR HIS PRO GLY ALA VAL PRO GLU MET SEQRES 17 A 342 LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SER GLU SEQRES 18 A 342 GLU ALA ILE ASN THR ILE TYR GLU LEU GLY LYS LYS ALA SEQRES 19 A 342 ARG GLY HIS ALA PHE LYS LEU PRO ALA GLU LEU ILE GLY SEQRES 20 A 342 PRO VAL CYS ASP MET CYS ALA ALA LEU THR ALA ILE THR SEQRES 21 A 342 TYR ALA GLY LEU LEU VAL TYR ARG ASP ALA VAL MET ASN SEQRES 22 A 342 ILE LEU GLY ALA PRO ALA GLY PHE SER GLN MET MET ALA SEQRES 23 A 342 THR GLU SER LEU GLU GLN ILE THR ALA TYR MET LYS LYS SEQRES 24 A 342 VAL GLY ILE LYS ASN LEU GLU GLU ASN LEU ASP PRO GLY SEQRES 25 A 342 VAL PHE LEU GLY THR ALA ASP SER MET ASN PHE GLY PRO SEQRES 26 A 342 ILE ALA GLU ILE LEU PRO THR VAL LEU LYS SER LEU GLU SEQRES 27 A 342 LYS ARG ALA LYS SEQRES 1 C 342 MET THR ILE LYS LYS VAL ALA ILE LEU GLY ALA GLY CYS SEQRES 2 C 342 TYR ARG THR HIS SER ALA THR GLY ILE THR ASN PHE ALA SEQRES 3 C 342 ARG ALA CYS GLU VAL ALA GLU MET VAL GLY LYS PRO GLU SEQRES 4 C 342 ILE ALA MET THR HIS SER THR ILE ALA MET ALA ALA GLU SEQRES 5 C 342 LEU LYS TYR LEU ALA GLY ILE ASP ASN ILE VAL ILE SER SEQRES 6 C 342 ASP PRO SER PHE ALA GLY GLU PHE THR VAL VAL LYS ASP SEQRES 7 C 342 PHE ASP TYR ASN GLU VAL ILE LYS ALA HIS LYS GLU ASN SEQRES 8 C 342 PRO GLU THR ILE MET PRO LYS ILE ARG GLU LYS VAL ASN SEQRES 9 C 342 GLU LEU ALA LYS THR VAL PRO LYS PRO PRO LYS GLY ALA SEQRES 10 C 342 ILE HIS PHE VAL HIS PRO GLU ASP LEU GLY LEU LYS VAL SEQRES 11 C 342 THR THR ASP ASP ARG GLU ALA VAL ARG ASP ALA ASP LEU SEQRES 12 C 342 ILE ILE THR TRP LEU PRO LYS GLY ASP MET GLN LYS GLY SEQRES 13 C 342 ILE ILE GLU LYS PHE ALA GLY ASP ILE LYS GLN GLY ALA SEQRES 14 C 342 ILE ILE THR HIS ALA CYS THR ILE PRO THR THR LEU PHE SEQRES 15 C 342 TYR LYS ILE PHE GLU GLU LEU GLY ILE ALA ASP LYS VAL SEQRES 16 C 342 GLU VAL THR SER TYR HIS PRO GLY ALA VAL PRO GLU MET SEQRES 17 C 342 LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SER GLU SEQRES 18 C 342 GLU ALA ILE ASN THR ILE TYR GLU LEU GLY LYS LYS ALA SEQRES 19 C 342 ARG GLY HIS ALA PHE LYS LEU PRO ALA GLU LEU ILE GLY SEQRES 20 C 342 PRO VAL CYS ASP MET CYS ALA ALA LEU THR ALA ILE THR SEQRES 21 C 342 TYR ALA GLY LEU LEU VAL TYR ARG ASP ALA VAL MET ASN SEQRES 22 C 342 ILE LEU GLY ALA PRO ALA GLY PHE SER GLN MET MET ALA SEQRES 23 C 342 THR GLU SER LEU GLU GLN ILE THR ALA TYR MET LYS LYS SEQRES 24 C 342 VAL GLY ILE LYS ASN LEU GLU GLU ASN LEU ASP PRO GLY SEQRES 25 C 342 VAL PHE LEU GLY THR ALA ASP SER MET ASN PHE GLY PRO SEQRES 26 C 342 ILE ALA GLU ILE LEU PRO THR VAL LEU LYS SER LEU GLU SEQRES 27 C 342 LYS ARG ALA LYS HET 5GP A 401 24 HET FMT A 402 3 HET FMT A 403 3 HET FMT A 404 3 HET FMT A 405 3 HET FMT A 406 3 HET 5GP C 401 24 HET FMT C 402 3 HET FMT C 403 3 HET FMT C 404 3 HET GOL C 405 6 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM FMT FORMIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 5GP 2(C10 H14 N5 O8 P) FORMUL 4 FMT 8(C H2 O2) FORMUL 13 GOL C3 H8 O3 FORMUL 14 HOH *640(H2 O) HELIX 1 AA1 TYR A 14 THR A 20 1 7 HELIX 2 AA2 PHE A 25 GLY A 36 1 12 HELIX 3 AA3 LYS A 37 ALA A 41 5 5 HELIX 4 AA4 HIS A 44 LEU A 56 1 13 HELIX 5 AA5 PRO A 67 GLY A 71 5 5 HELIX 6 AA6 ASP A 80 GLU A 90 1 11 HELIX 7 AA7 ASN A 91 THR A 94 5 4 HELIX 8 AA8 ILE A 95 LYS A 108 1 14 HELIX 9 AA9 HIS A 122 GLY A 127 5 6 HELIX 10 AB1 ASP A 133 ARG A 139 1 7 HELIX 11 AB2 MET A 153 ALA A 162 1 10 HELIX 12 AB3 GLY A 163 ILE A 165 5 3 HELIX 13 AB4 PRO A 178 LEU A 189 1 12 HELIX 14 AB5 ILE A 191 VAL A 195 5 5 HELIX 15 AB6 SER A 220 GLY A 236 1 17 HELIX 16 AB7 LEU A 245 ASP A 251 1 7 HELIX 17 AB8 CYS A 253 ILE A 274 1 22 HELIX 18 AB9 PRO A 278 GLY A 301 1 24 HELIX 19 AC1 ASN A 304 LEU A 309 1 6 HELIX 20 AC2 ASP A 310 GLY A 316 5 7 HELIX 21 AC3 THR A 317 ASN A 322 5 6 HELIX 22 AC4 PHE A 323 GLU A 328 5 6 HELIX 23 AC5 ILE A 329 ARG A 340 1 12 HELIX 24 AC6 TYR C 14 THR C 20 1 7 HELIX 25 AC7 PHE C 25 GLY C 36 1 12 HELIX 26 AC8 LYS C 37 ALA C 41 5 5 HELIX 27 AC9 HIS C 44 LEU C 56 1 13 HELIX 28 AD1 PRO C 67 GLY C 71 5 5 HELIX 29 AD2 ASP C 80 LYS C 89 1 10 HELIX 30 AD3 GLU C 90 THR C 94 5 5 HELIX 31 AD4 ILE C 95 ALA C 107 1 13 HELIX 32 AD5 HIS C 122 GLY C 127 5 6 HELIX 33 AD6 ASP C 133 ARG C 139 1 7 HELIX 34 AD7 MET C 153 ALA C 162 1 10 HELIX 35 AD8 GLY C 163 ILE C 165 5 3 HELIX 36 AD9 PRO C 178 LEU C 189 1 12 HELIX 37 AE1 ILE C 191 VAL C 195 5 5 HELIX 38 AE2 SER C 220 GLY C 236 1 17 HELIX 39 AE3 LEU C 245 ASP C 251 1 7 HELIX 40 AE4 CYS C 253 ILE C 274 1 22 HELIX 41 AE5 PRO C 278 GLY C 301 1 24 HELIX 42 AE6 ASN C 304 LEU C 309 1 6 HELIX 43 AE7 ASP C 310 ASN C 322 5 13 HELIX 44 AE8 PHE C 323 GLU C 328 5 6 HELIX 45 AE9 ILE C 329 ARG C 340 1 12 SHEET 1 AA1 6 LYS A 129 THR A 131 0 SHEET 2 AA1 6 ASN A 61 SER A 65 1 N ILE A 64 O LYS A 129 SHEET 3 AA1 6 LYS A 5 LEU A 9 1 N ILE A 8 O SER A 65 SHEET 4 AA1 6 LEU A 143 THR A 146 1 O LEU A 143 N ALA A 7 SHEET 5 AA1 6 ILE A 170 HIS A 173 1 O THR A 172 N ILE A 144 SHEET 6 AA1 6 GLU A 196 SER A 199 1 O GLU A 196 N ILE A 171 SHEET 1 AA2 2 GLU A 72 VAL A 75 0 SHEET 2 AA2 2 GLY A 116 HIS A 119 1 O HIS A 119 N THR A 74 SHEET 1 AA3 2 VAL A 212 GLU A 216 0 SHEET 2 AA3 2 ALA A 238 PRO A 242 1 O PHE A 239 N ILE A 214 SHEET 1 AA4 6 LYS C 129 THR C 131 0 SHEET 2 AA4 6 ASN C 61 SER C 65 1 N ILE C 64 O LYS C 129 SHEET 3 AA4 6 LYS C 5 LEU C 9 1 N ILE C 8 O SER C 65 SHEET 4 AA4 6 LEU C 143 THR C 146 1 O ILE C 145 N LEU C 9 SHEET 5 AA4 6 ILE C 170 HIS C 173 1 O THR C 172 N ILE C 144 SHEET 6 AA4 6 GLU C 196 SER C 199 1 O GLU C 196 N ILE C 171 SHEET 1 AA5 2 GLU C 72 VAL C 75 0 SHEET 2 AA5 2 GLY C 116 HIS C 119 1 O HIS C 119 N THR C 74 SHEET 1 AA6 2 VAL C 212 GLU C 216 0 SHEET 2 AA6 2 ALA C 238 PRO C 242 1 O PHE C 239 N ILE C 214 CISPEP 1 PRO A 113 PRO A 114 0 4.07 CISPEP 2 PRO C 113 PRO C 114 0 3.78 SITE 1 AC1 19 GLY A 10 GLY A 12 SER A 65 ASP A 66 SITE 2 AC1 19 PRO A 67 PRO A 113 PRO A 114 ASP A 134 SITE 3 AC1 19 TRP A 147 LEU A 148 PRO A 149 ILE A 157 SITE 4 AC1 19 HOH A 530 HOH A 587 HOH A 589 HOH A 615 SITE 5 AC1 19 HOH A 621 HOH A 655 HOH A 694 SITE 1 AC2 7 SER A 320 HOH A 507 HOH A 531 ALA C 204 SITE 2 AC2 7 VAL C 205 MET C 208 LYS C 209 SITE 1 AC3 3 ASP A 152 HOH A 553 MET C 284 SITE 1 AC4 4 ASN A 91 PRO A 92 HOH A 572 HOH A 679 SITE 1 AC5 2 LYS A 89 HOH A 608 SITE 1 AC6 3 ASP A 78 LYS A 98 HOH A 594 SITE 1 AC7 21 LEU C 9 GLY C 10 GLY C 12 SER C 65 SITE 2 AC7 21 ASP C 66 PRO C 67 PRO C 113 PRO C 114 SITE 3 AC7 21 ASP C 134 TRP C 147 LEU C 148 PRO C 149 SITE 4 AC7 21 ILE C 157 HOH C 515 HOH C 516 HOH C 567 SITE 5 AC7 21 HOH C 573 HOH C 588 HOH C 640 HOH C 658 SITE 6 AC7 21 HOH C 673 SITE 1 AC8 3 GLY C 58 HOH C 575 HOH C 632 SITE 1 AC9 4 LYS A 299 PRO C 242 GLU C 244 HOH C 629 SITE 1 AD1 3 GLU C 30 HIS C 237 HOH C 529 SITE 1 AD2 5 ILE A 274 LEU A 275 THR C 16 ALA C 19 SITE 2 AD2 5 HOH C 521 CRYST1 67.805 57.058 95.125 90.00 91.43 90.00 P 1 21 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 0.014748 0.000000 0.000368 0.00000 SCALE2 0.000000 0.017526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010516 0.00000