HEADER OXIDOREDUCTASE 20-JUL-17 5Y1F TITLE MONOMERIC L-THREONINE 3-DEHYDROGENASE FROM METAGENOME DATABASE (NAD+ TITLE 2 BOUND FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD DEPENDENT EPIMERASE/DEHYDRATASE FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED ARCHAEON MEDDCM-OCT-S05-C57; SOURCE 3 ORGANISM_TAXID: 743092; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDROGENASE, NAD+, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.MOTOYAMA,S.NAKANO,Y.YAMAMOTO,H.TOKIWA,Y.ASANO,S.ITO REVDAT 2 22-NOV-23 5Y1F 1 REMARK REVDAT 1 15-NOV-17 5Y1F 0 JRNL AUTH T.MOTOYAMA,S.NAKANO,Y.YAMAMOTO,H.TOKIWA,Y.ASANO,S.ITO JRNL TITL PRODUCT RELEASE MECHANISM ASSOCIATED WITH STRUCTURAL CHANGES JRNL TITL 2 IN MONOMERIC L-THREONINE 3-DEHYDROGENASE. JRNL REF BIOCHEMISTRY V. 56 5758 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28992410 JRNL DOI 10.1021/ACS.BIOCHEM.7B00832 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 72123 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3743 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5681 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 320 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2499 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 426 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.656 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2695 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2487 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3667 ; 1.652 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5774 ; 0.802 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 330 ; 6.780 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;38.026 ;25.420 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 481 ;14.959 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.639 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 390 ; 0.271 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3077 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 599 ; 0.003 ; 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): 1293 ; 1.359 ; 1.103 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1292 ; 1.349 ; 1.101 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1632 ; 1.892 ; 1.658 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1633 ; 1.893 ; 1.660 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1402 ; 3.204 ; 1.410 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1403 ; 3.203 ; 1.409 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2036 ; 4.605 ; 1.993 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3667 ; 6.585 ;11.321 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3368 ; 6.249 ;10.180 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 5Y1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-16 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75876 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 54.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.28 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3WMX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350, 0.2M SODIUM REMARK 280 FLUORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 56.74700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.46350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.74700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.46350 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 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 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 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 O HOH A 864 O HOH A 887 1.95 REMARK 500 O HOH A 658 O HOH A 803 1.97 REMARK 500 O HOH A 550 O HOH A 827 2.00 REMARK 500 OE2 GLU A 287 O HOH A 502 2.04 REMARK 500 O HOH A 635 O HOH A 795 2.04 REMARK 500 O HOH A 509 O HOH A 516 2.05 REMARK 500 O HOH A 699 O HOH A 878 2.07 REMARK 500 ND2 ASN A 201 O HOH A 503 2.11 REMARK 500 O HOH A 725 O HOH A 755 2.14 REMARK 500 NZ LYS A 22 OD2 ASP A 221 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 559 O HOH A 569 4545 1.30 REMARK 500 NZ LYS A 45 OE2 GLU A 298 4546 1.91 REMARK 500 OD1 ASN A 201 NH1 ARG A 281 4545 1.91 REMARK 500 O HOH A 503 O HOH A 794 4545 1.98 REMARK 500 O HOH A 581 O HOH A 822 4545 2.05 REMARK 500 O HOH A 533 O HOH A 695 4555 2.09 REMARK 500 O HOH A 613 O HOH A 848 2555 2.14 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 ASN A 59 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 LYS A 289 CD - CE - NZ ANGL. DEV. = 14.5 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 ASN A 38 72.62 -116.09 REMARK 500 HIS A 40 53.86 -105.07 REMARK 500 SER A 110 -152.05 -109.35 REMARK 500 HIS A 230 -74.12 -126.25 REMARK 500 ASN A 232 41.21 -147.54 REMARK 500 SER A 237 -73.54 -142.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 38 TYR A 39 -146.78 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 924 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 925 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 926 DISTANCE = 6.76 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 DBREF 5Y1F A 1 308 UNP D6PBM7 D6PBM7_9ARCH 1 308 SEQADV 5Y1F MET A -19 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F GLY A -18 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F SER A -17 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F SER A -16 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A -15 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A -14 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A -13 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A -12 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A -11 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A -10 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F SER A -9 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F SER A -8 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F GLY A -7 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F LEU A -6 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F VAL A -5 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F PRO A -4 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F ARG A -3 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F GLY A -2 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F SER A -1 UNP D6PBM7 EXPRESSION TAG SEQADV 5Y1F HIS A 0 UNP D6PBM7 EXPRESSION TAG SEQRES 1 A 328 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 328 LEU VAL PRO ARG GLY SER HIS MET ILE LEU VAL THR GLY SEQRES 3 A 328 ALA LEU GLY GLN ILE GLY THR GLU LEU VAL LEU ALA LEU SEQRES 4 A 328 GLN GLU LYS TYR GLY ASN ASP LYS ILE ILE ALA SER ASP SEQRES 5 A 328 LEU LYS GLU PRO GLU ASN TYR HIS CYS LYS PHE GLU LYS SEQRES 6 A 328 CYS ASP ILE ARG ASP ILE GLU THR TYR GLU ARG ILE ASN SEQRES 7 A 328 ASN GLU ASN LYS ILE GLU ILE VAL TYR HIS LEU ALA ALA SEQRES 8 A 328 ILE LEU SER ALA ALA GLY GLU LYS ASN PRO GLU LEU CYS SEQRES 9 A 328 HIS ASP VAL ASN TYR ASN GLY LEU GLU ASN VAL LEU LYS SEQRES 10 A 328 THR ALA LYS LYS TYR ASN GLN LYS LEU PHE CYS PRO SER SEQRES 11 A 328 SER ILE ALA VAL PHE GLY PRO ASP VAL PRO LYS GLU MET SEQRES 12 A 328 THR PRO GLN ASN VAL GLU LEU ASN PRO LYS THR VAL TYR SEQRES 13 A 328 GLY ILE THR LYS VAL LYS GLY GLU GLU LEU CYS ASP THR SEQRES 14 A 328 TYR PHE LYS GLU HIS GLY ILE ASP VAL ARG GLY ILE ARG SEQRES 15 A 328 TYR PRO GLY LEU ILE SER TRP LYS HIS LYS PRO SER GLY SEQRES 16 A 328 GLY THR THR ASP TYR ALA VAL GLU MET TYR PHE ASP ALA SEQRES 17 A 328 VAL GLU SER GLY LYS TYR GLU CYS PHE VAL ASN ARG ASN SEQRES 18 A 328 THR ARG LEU PRO MET MET PHE MET ASP ASP ALA ILE ARG SEQRES 19 A 328 ALA THR LEU GLU LEU MET ASP ALA PRO LEU ASP SER LEU SEQRES 20 A 328 ASN TYR HIS SER ASN TYR ASN LEU SER SER MET SER PHE SEQRES 21 A 328 SER ALA GLU GLU LEU GLU LYS GLU ILE SER ALA HIS VAL SEQRES 22 A 328 ASP PHE ASN CYS LEU TYR LYS PRO ASP TYR ARG GLN ASP SEQRES 23 A 328 ILE ALA ASP THR TRP PRO ILE SER ILE ASN ASP ASP ASP SEQRES 24 A 328 ALA ARG LYS ASP TRP GLY TRP GLU PRO LYS PHE ASP ILE SEQRES 25 A 328 SER LYS MET THR GLU GLU MET ILE THR ASN LEU ARG ARG SEQRES 26 A 328 LEU ASN GLU HET NAD A 401 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 HOH *426(H2 O) HELIX 1 AA1 GLY A 9 GLY A 24 1 16 HELIX 2 AA2 ASP A 50 ASN A 61 1 12 HELIX 3 AA3 LEU A 73 ASN A 80 1 8 HELIX 4 AA4 ASN A 80 ASN A 103 1 24 HELIX 5 AA5 ALA A 113 PHE A 115 5 3 HELIX 6 AA6 THR A 134 GLY A 155 1 22 HELIX 7 AA7 THR A 178 GLY A 192 1 15 HELIX 8 AA8 MET A 209 ALA A 222 1 14 HELIX 9 AA9 PRO A 223 LEU A 227 5 5 HELIX 10 AB1 ALA A 242 ALA A 251 1 10 HELIX 11 AB2 TYR A 263 ASP A 269 1 7 HELIX 12 AB3 ASP A 277 GLY A 285 1 9 HELIX 13 AB4 ASP A 291 ASN A 307 1 17 SHEET 1 AA1 6 LYS A 42 LYS A 45 0 SHEET 2 AA1 6 ILE A 28 ASP A 32 1 N ALA A 30 O LYS A 42 SHEET 3 AA1 6 MET A 1 THR A 5 1 N ILE A 2 O ILE A 29 SHEET 4 AA1 6 ILE A 63 HIS A 68 1 O TYR A 67 N LEU A 3 SHEET 5 AA1 6 LYS A 105 PHE A 107 1 O PHE A 107 N HIS A 68 SHEET 6 AA1 6 VAL A 158 ARG A 159 1 O ARG A 159 N LEU A 106 SHEET 1 AA2 3 SER A 110 SER A 111 0 SHEET 2 AA2 3 ILE A 161 TYR A 163 1 O ILE A 161 N SER A 110 SHEET 3 AA2 3 TYR A 233 ASN A 234 1 O TYR A 233 N ARG A 162 SHEET 1 AA3 3 GLY A 165 ILE A 167 0 SHEET 2 AA3 3 ARG A 203 PHE A 208 1 O PRO A 205 N GLY A 165 SHEET 3 AA3 3 MET A 238 SER A 241 -1 O MET A 238 N MET A 206 SHEET 1 AA4 2 LYS A 193 CYS A 196 0 SHEET 2 AA4 2 ASN A 256 TYR A 259 1 O LEU A 258 N CYS A 196 SITE 1 AC1 34 GLY A 6 GLY A 9 GLN A 10 ILE A 11 SITE 2 AC1 34 ASP A 32 LEU A 33 CYS A 46 ASP A 47 SITE 3 AC1 34 ILE A 48 ARG A 49 LEU A 69 ALA A 70 SITE 4 AC1 34 ALA A 71 LEU A 73 VAL A 87 PRO A 109 SITE 5 AC1 34 SER A 110 SER A 111 TYR A 136 LYS A 140 SITE 6 AC1 34 TYR A 163 PRO A 164 LEU A 166 HOH A 509 SITE 7 AC1 34 HOH A 516 HOH A 534 HOH A 541 HOH A 553 SITE 8 AC1 34 HOH A 583 HOH A 600 HOH A 647 HOH A 701 SITE 9 AC1 34 HOH A 707 HOH A 785 CRYST1 113.494 48.927 56.364 90.00 104.71 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 0.008811 0.000000 0.002313 0.00000 SCALE2 0.000000 0.020439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018343 0.00000