HEADER METAL BINDING PROTEIN 17-MAR-15 4YT4 TITLE IRON GUANYLYLPYRIDINOL (FEGP) COFACTOR-RECONSTITUTED HMDII FROM TITLE 2 METHANOCALDOCOCCUS JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: H(2)-FORMING METHYLENETETRAHYDROMETHANOPTERIN COMPND 3 DEHYDROGENASE-RELATED PROTEIN MJ1338; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: ROSSMANN-LIKE DOMAIN, UNP RESIDUES 1-353; COMPND 6 SYNONYM: HMDII; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ1338; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS ROSSMANN-LIKE FOLD, [FE]-HYDROGENASE ANALOG, OXIDOREDUCTASE, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.FUJISHIRO,U.ERMLER,S.SHIMA REVDAT 3 01-MAY-24 4YT4 1 REMARK REVDAT 2 09-SEP-15 4YT4 1 JRNL REVDAT 1 01-JUL-15 4YT4 0 JRNL AUTH T.FUJISHIRO,K.ATAKA,U.ERMLER,S.SHIMA JRNL TITL TOWARDS A FUNCTIONAL IDENTIFICATION OF CATALYTICALLY JRNL TITL 2 INACTIVE [FE]-HYDROGENASE PARALOGS. JRNL REF FEBS J. V. 282 3412 2015 JRNL REFN ISSN 1742-464X JRNL PMID 26094576 JRNL DOI 10.1111/FEBS.13351 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 16788 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 : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 884 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1136 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -0.36000 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): 0.286 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.552 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2691 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3651 ; 1.896 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 344 ; 6.371 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;40.414 ;25.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 488 ;17.506 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;24.481 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 430 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1937 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1379 ; 1.413 ; 2.892 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1722 ; 2.304 ; 4.330 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1312 ; 2.871 ; 3.409 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 12 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 52 REMARK 3 RESIDUE RANGE : A 53 A 68 REMARK 3 RESIDUE RANGE : A 69 A 92 REMARK 3 RESIDUE RANGE : A 93 A 114 REMARK 3 RESIDUE RANGE : A 115 A 130 REMARK 3 RESIDUE RANGE : A 131 A 153 REMARK 3 RESIDUE RANGE : A 154 A 182 REMARK 3 RESIDUE RANGE : A 183 A 240 REMARK 3 RESIDUE RANGE : A 241 A 271 REMARK 3 RESIDUE RANGE : A 272 A 301 REMARK 3 RESIDUE RANGE : A 302 A 322 REMARK 3 RESIDUE RANGE : A 323 A 355 REMARK 3 ORIGIN FOR THE GROUP (A): -9.9210 30.0303 -7.5620 REMARK 3 T TENSOR REMARK 3 T11: 0.0637 T22: 0.0470 REMARK 3 T33: 0.0642 T12: -0.0118 REMARK 3 T13: 0.0268 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.8465 L22: 1.0352 REMARK 3 L33: 0.3874 L12: -0.6111 REMARK 3 L13: -0.5510 L23: 0.5082 REMARK 3 S TENSOR REMARK 3 S11: -0.0344 S12: -0.0156 S13: -0.2158 REMARK 3 S21: -0.0389 S22: -0.0947 S23: 0.1426 REMARK 3 S31: -0.0113 S32: 0.0016 S33: 0.1291 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: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4YT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : A DOUBLE-CRYSTAL SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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: HMDII FROM M. JANNASCHII REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% (V/V) PEG200, 0.1 M NA/K REMARK 280 -PHOSPHATE, 0.2 M NACL, PH 6.2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 91.71500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.90500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.85750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.90500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.90500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 137.57250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.90500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.90500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.85750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.90500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.90500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 137.57250 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 91.71500 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: 11510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -115.0 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 0.000000 1.000000 0.000000 -59.81000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 59.81000 REMARK 350 BIOMT3 2 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 ARG A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 ARG A 5 REMARK 465 LYS A 6 REMARK 465 ILE A 7 REMARK 465 LYS A 8 REMARK 465 VAL A 9 REMARK 465 ASP A 10 REMARK 465 PRO A 356 REMARK 465 ASN A 357 REMARK 465 SER A 358 REMARK 465 SER A 359 REMARK 465 SER A 360 REMARK 465 VAL A 361 REMARK 465 ASP A 362 REMARK 465 LYS A 363 REMARK 465 LEU A 364 REMARK 465 ALA A 365 REMARK 465 ALA A 366 REMARK 465 ALA A 367 REMARK 465 LEU A 368 REMARK 465 GLU A 369 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 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 PHE A 99 56.92 -96.80 REMARK 500 ALA A 121 151.66 -45.91 REMARK 500 THR A 126 -144.20 -119.94 REMARK 500 THR A 144 -77.57 -116.69 REMARK 500 ALA A 158 164.93 171.34 REMARK 500 ASN A 272 95.11 58.34 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 FE9 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 127 SG REMARK 620 2 FE9 A 401 N1 89.1 REMARK 620 3 FE9 A 401 C1F 170.4 94.6 REMARK 620 4 FE9 A 401 C8 76.0 102.0 94.5 REMARK 620 5 FE9 A 401 C2F 91.3 178.9 85.2 79.1 REMARK 620 6 FE9 A 401 O1 94.5 97.9 93.8 157.7 81.0 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 FE9 A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YT2 RELATED DB: PDB REMARK 900 APO-FORM REMARK 900 RELATED ID: 4YTE RELATED DB: PDB REMARK 900 RELATED ID: 4YT5 RELATED DB: PDB REMARK 900 RELATED ID: 4YT8 RELATED DB: PDB DBREF 4YT4 A 1 353 UNP Q58734 HMDY_METJA 1 353 SEQADV 4YT4 ALA A 354 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 ASP A 355 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 PRO A 356 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 ASN A 357 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 SER A 358 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 SER A 359 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 SER A 360 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 VAL A 361 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 ASP A 362 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 LYS A 363 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 LEU A 364 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 ALA A 365 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 ALA A 366 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 ALA A 367 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 LEU A 368 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 GLU A 369 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 HIS A 370 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 HIS A 371 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 HIS A 372 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 HIS A 373 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 HIS A 374 UNP Q58734 EXPRESSION TAG SEQADV 4YT4 HIS A 375 UNP Q58734 EXPRESSION TAG SEQRES 1 A 375 MET ARG ASN ILE ARG LYS ILE LYS VAL ASP ASN MET LYS SEQRES 2 A 375 VAL SER VAL TYR GLY ALA GLY ASN GLN ASN LEU TYR ILE SEQRES 3 A 375 ASN LYS LEU ASN LEU PRO GLU LYS PHE GLY GLY GLU PRO SEQRES 4 A 375 PRO TYR GLY GLY SER ARG MET ALA ILE GLU PHE ALA GLU SEQRES 5 A 375 ALA GLY HIS ASP VAL VAL LEU ALA GLU PRO ASN LYS ASN SEQRES 6 A 375 ILE MET SER ASP ASP LEU TRP LYS LYS VAL GLU ASP ALA SEQRES 7 A 375 GLY VAL LYS VAL VAL SER ASP ASP VAL GLU ALA ALA LYS SEQRES 8 A 375 HIS GLY GLU ILE HIS VAL LEU PHE THR PRO PHE GLY LYS SEQRES 9 A 375 ALA THR PHE ARG ILE ALA LYS THR ILE ILE GLU HIS VAL SEQRES 10 A 375 PRO GLU ASN ALA VAL ILE CYS ASN THR CYS THR VAL SER SEQRES 11 A 375 PRO VAL VAL LEU TYR TYR SER LEU GLU PRO ILE LEU ARG SEQRES 12 A 375 THR LYS ARG LYS ASP VAL GLY ILE SER SER MET HIS PRO SEQRES 13 A 375 ALA ALA VAL PRO GLY THR PRO GLN HIS GLY HIS TYR VAL SEQRES 14 A 375 ILE GLY GLY LYS THR THR ASP GLY LYS GLU LEU ALA THR SEQRES 15 A 375 GLU GLU GLN ILE LYS LYS ALA VAL GLU LEU ALA LYS SER SEQRES 16 A 375 ALA GLY LYS GLU ALA TYR VAL VAL PRO ALA ASP VAL SER SEQRES 17 A 375 SER VAL VAL ALA ASP MET GLY SER LEU VAL THR ALA VAL SEQRES 18 A 375 ALA LEU SER GLY VAL LEU ASP TYR TYR THR VAL GLY ARG SEQRES 19 A 375 LYS ILE ILE ASN ALA PRO LYS LYS MET ILE GLU GLN GLN SEQRES 20 A 375 VAL ILE MET THR LEU GLN THR MET ALA SER LEU VAL GLU SEQRES 21 A 375 THR SER GLY ILE GLU GLY MET VAL LYS ALA LEU ASN PRO SEQRES 22 A 375 GLU LEU LEU ILE ARG SER ALA SER SER MET LYS LEU LEU SEQRES 23 A 375 ASP ARG GLN LYS ASP LEU ASP ALA ALA LEU GLU ILE LEU SEQRES 24 A 375 GLN ASN LEU ASP GLU THR LEU LYS ALA GLU VAL GLU LYS SEQRES 25 A 375 ALA GLU ILE LYS PRO THR THR LEU VAL ALA ALA GLN SER SEQRES 26 A 375 LEU VAL LYS GLU ILE LYS THR LEU ILE GLY GLY ALA ALA SEQRES 27 A 375 ALA GLU GLY ALA ILE LYS ARG SER ALA ARG LYS LEU PHE SEQRES 28 A 375 GLU HIS ALA ASP PRO ASN SER SER SER VAL ASP LYS LEU SEQRES 29 A 375 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET FE9 A 401 42 HETNAM FE9 IRON-GUANYLYL PYRIDINOL COFACTOR FORMUL 2 FE9 C21 H23 FE N6 O13 P S 4+ FORMUL 3 HOH *108(H2 O) HELIX 1 AA1 ASN A 21 ASN A 27 1 7 HELIX 2 AA2 ASN A 30 PHE A 35 1 6 HELIX 3 AA3 GLY A 42 ALA A 53 1 12 HELIX 4 AA4 ASN A 63 MET A 67 5 5 HELIX 5 AA5 SER A 68 ALA A 78 1 11 HELIX 6 AA6 ASP A 85 GLY A 93 1 9 HELIX 7 AA7 GLY A 103 GLU A 115 1 13 HELIX 8 AA8 SER A 130 THR A 144 1 15 HELIX 9 AA9 THR A 182 ALA A 196 1 15 HELIX 10 AB1 ALA A 205 ASP A 213 1 9 HELIX 11 AB2 GLY A 215 ILE A 236 1 22 HELIX 12 AB3 PRO A 240 ASN A 272 1 33 HELIX 13 AB4 ASN A 272 SER A 282 1 11 HELIX 14 AB5 GLN A 289 ASN A 301 1 13 HELIX 15 AB6 THR A 305 ALA A 313 1 9 HELIX 16 AB7 ALA A 322 ILE A 334 1 13 HELIX 17 AB8 GLY A 335 GLU A 352 1 18 SHEET 1 AA1 6 LYS A 81 VAL A 83 0 SHEET 2 AA1 6 ASP A 56 ALA A 60 1 N LEU A 59 O LYS A 81 SHEET 3 AA1 6 LYS A 13 TYR A 17 1 N VAL A 16 O VAL A 58 SHEET 4 AA1 6 ILE A 95 LEU A 98 1 O VAL A 97 N TYR A 17 SHEET 5 AA1 6 VAL A 122 ASN A 125 1 O CYS A 124 N HIS A 96 SHEET 6 AA1 6 GLY A 150 SER A 153 1 O GLY A 150 N ILE A 123 SHEET 1 AA2 2 HIS A 167 GLY A 172 0 SHEET 2 AA2 2 GLU A 199 PRO A 204 1 O TYR A 201 N ILE A 170 LINK SG CYS A 127 FE FE9 A 401 1555 1555 2.38 CISPEP 1 PRO A 39 PRO A 40 0 1.34 SITE 1 AC1 23 TYR A 17 GLY A 18 ALA A 19 GLY A 20 SITE 2 AC1 23 ASN A 21 TYR A 25 ALA A 60 GLU A 61 SITE 3 AC1 23 PRO A 62 ASP A 86 PHE A 99 THR A 100 SITE 4 AC1 23 PRO A 101 ARG A 108 ILE A 109 THR A 126 SITE 5 AC1 23 CYS A 127 HIS A 155 PRO A 156 ALA A 158 SITE 6 AC1 23 VAL A 159 HOH A 588 HOH A 594 CRYST1 59.810 59.810 183.430 90.00 90.00 90.00 P 41 21 2 8 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 0.016720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005452 0.00000