HEADER OXIDOREDUCTASE 26-OCT-23 8QZA TITLE D-2-HYDROXYACID DEHYDROGENASE (D2-HDH) FROM HALOFERAX MEDITERRANEI TITLE 2 APO-ENZYME (2.25 A RESOLUTION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-2-HYDROXYACID DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOFERAX MEDITERRANEI; SOURCE 3 ORGANISM_TAXID: 2252; SOURCE 4 GENE: DDH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HALOPHILIC ADAPTATION DOMAIN CLOSURE MECHANISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.J.BAKER,J.R.BARRETT,A.A.A.B.DAKHIL,J.DOMENECH,C.BISSON,N.PRAMANPOL, AUTHOR 2 S.E.SEDELNIKOVA,J.FERRER,D.W.RICE REVDAT 2 20-AUG-25 8QZA 1 JRNL REVDAT 1 06-AUG-25 8QZA 0 JRNL AUTH J.DOMENECH,N.PRAMANPOL,C.BISSON,S.E.SEDELNIKOVA,J.R.BARRETT, JRNL AUTH 2 A.A.A.B.DAKHIL,V.MYKHAYLYK,A.S.ABDELHAMEED,S.E.HARDING, JRNL AUTH 3 D.W.RICE,P.J.BAKER,J.FERRER JRNL TITL POTASSIUM BINDING BY CARBONYL CLUSTERS, HALOPHILIC JRNL TITL 2 ADAPTATION AND CATALYSIS OF HALOFERAX MEDITERRANEI JRNL TITL 3 D-2-HYDROXYACID DEHYDROGENASE. JRNL REF COMMUN BIOL V. 8 1170 2025 JRNL REFN ESSN 2399-3642 JRNL PMID 40770045 JRNL DOI 10.1038/S42003-025-08587-7 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 32639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1645 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1930 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.65000 REMARK 3 B22 (A**2) : 2.00600 REMARK 3 B33 (A**2) : -0.50800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.12600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.277 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.083 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4804 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4376 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6560 ; 1.939 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10066 ; 0.744 ; 1.573 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 614 ; 8.219 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 40 ;11.921 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 708 ;16.339 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 744 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5828 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1072 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 916 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 27 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2355 ; 0.164 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 121 ; 0.108 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.119 ; 0.200 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): 2462 ; 7.374 ; 5.293 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2462 ; 7.374 ; 5.292 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3074 ;10.670 ; 9.505 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3075 ;10.669 ; 9.508 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2342 ; 7.645 ; 5.794 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2343 ; 7.644 ; 5.797 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3486 ;11.161 ;10.433 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3487 ;11.160 ;10.435 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 308 NULL REMARK 3 1 A 1 A 308 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 308 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2376 0.1607 16.2685 REMARK 3 T TENSOR REMARK 3 T11: 0.0056 T22: 0.2045 REMARK 3 T33: 0.1553 T12: -0.0121 REMARK 3 T13: 0.0140 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.1708 L22: 0.0303 REMARK 3 L33: 0.0384 L12: -0.1515 REMARK 3 L13: -0.1182 L23: 0.0006 REMARK 3 S TENSOR REMARK 3 S11: 0.0414 S12: 0.2012 S13: 0.0835 REMARK 3 S21: -0.0025 S22: -0.0499 S23: -0.0359 REMARK 3 S31: -0.0111 S32: 0.0405 S33: 0.0085 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -4.2414 -6.2181 38.0431 REMARK 3 T TENSOR REMARK 3 T11: 0.0430 T22: 0.1426 REMARK 3 T33: 0.1266 T12: -0.0101 REMARK 3 T13: 0.0219 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.7975 L22: 0.0510 REMARK 3 L33: 0.0870 L12: 0.1693 REMARK 3 L13: 0.1273 L23: 0.0420 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: -0.0731 S13: -0.0257 REMARK 3 S21: 0.0099 S22: -0.0301 S23: 0.0344 REMARK 3 S31: -0.0118 S32: -0.0631 S33: 0.0033 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8QZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1292134284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 29.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BLOCKS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFER: 20MM TRIS/HCL PH 8.0 REMARK 280 2MM EDTA 1M NACL CRYSTALLIZATION CONDITION: 0.1 M TRIS/HCL PH REMARK 280 8.0 0.5 M MAGNESIUM ACETATE 20% PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K 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 37.99300 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: 5740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 202 CD GLU A 202 OE2 0.086 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 109 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 165 NE - CZ - NH2 ANGL. DEV. = -3.6 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 PRO A 17 107.87 -53.68 REMARK 500 SER A 26 43.91 -89.04 REMARK 500 ASP A 27 50.32 -151.76 REMARK 500 TRP A 61 117.18 -160.34 REMARK 500 GLU A 71 39.39 -97.61 REMARK 500 ALA A 225 -97.88 -105.90 REMARK 500 ASP A 268 34.04 -92.74 REMARK 500 ALA B 196 34.02 -140.96 REMARK 500 ALA B 225 -100.83 -105.19 REMARK 500 PRO B 228 1.07 -68.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 108 0.10 SIDE CHAIN REMARK 500 ARG A 148 0.09 SIDE CHAIN REMARK 500 ARG A 166 0.10 SIDE CHAIN REMARK 500 ARG A 191 0.08 SIDE CHAIN REMARK 500 ARG A 291 0.09 SIDE CHAIN REMARK 500 ARG B 53 0.10 SIDE CHAIN REMARK 500 ARG B 108 0.09 SIDE CHAIN REMARK 500 ARG B 109 0.08 SIDE CHAIN REMARK 500 ARG B 126 0.08 SIDE CHAIN REMARK 500 ARG B 148 0.09 SIDE CHAIN REMARK 500 ARG B 166 0.13 SIDE CHAIN REMARK 500 ARG B 291 0.11 SIDE CHAIN 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 211 OE2 REMARK 620 2 HOH A 509 O 87.6 REMARK 620 3 HOH A 524 O 90.5 85.9 REMARK 620 4 HOH B 503 O 96.6 175.7 93.8 REMARK 620 5 HOH B 512 O 92.8 95.7 176.4 84.3 REMARK 620 6 HOH B 534 O 172.4 92.0 81.9 83.8 94.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 212 O REMARK 620 2 GLU A 213 O 78.0 REMARK 620 3 MET A 215 O 102.6 79.8 REMARK 620 4 ASP A 243 O 93.3 171.3 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 501 O REMARK 620 2 HOH A 502 O 100.8 REMARK 620 3 HOH A 503 O 174.1 81.7 REMARK 620 4 HOH A 508 O 94.4 87.5 80.4 REMARK 620 5 HOH B 502 O 90.1 89.2 95.3 174.9 REMARK 620 6 HOH B 535 O 90.1 160.7 86.0 75.8 106.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 510 O REMARK 620 2 HOH A 517 O 85.0 REMARK 620 3 HOH A 529 O 81.7 80.4 REMARK 620 4 GLU B 211 OE2 91.5 94.7 171.9 REMARK 620 5 HOH B 505 O 83.4 168.1 95.2 88.3 REMARK 620 6 HOH B 509 O 173.8 88.8 96.7 89.5 102.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 212 O REMARK 620 2 GLU B 213 O 80.9 REMARK 620 3 MET B 215 O 110.1 84.4 REMARK 620 4 ASP B 243 O 91.1 166.7 108.4 REMARK 620 5 HOH B 517 O 105.3 76.4 136.1 95.8 REMARK 620 N 1 2 3 4 DBREF 8QZA A 1 308 UNP Q2VEQ7 DDH_HALMT 1 308 DBREF 8QZA B 1 308 UNP Q2VEQ7 DDH_HALMT 1 308 SEQRES 1 A 308 MET HIS ILE GLU ARG LEU ALA VAL ASP GLU SER VAL GLY SEQRES 2 A 308 ARG ALA MET PRO PRO GLN ARG PHE ILE GLU ALA LEU SER SEQRES 3 A 308 ASP LEU GLY VAL PRO VAL GLU PHE ALA GLY GLU ASP GLU SEQRES 4 A 308 GLN PHE GLY PRO GLY ASP ALA VAL ALA SER PHE GLY HIS SEQRES 5 A 308 ARG ASP ALA PHE LEU ASP ALA ASP TRP VAL HIS CYS ILE SEQRES 6 A 308 ARG ALA GLY TYR ASP GLU PHE PRO VAL GLY VAL TYR GLU SEQRES 7 A 308 GLU ALA GLY THR TYR LEU THR ASN SER THR GLY ILE HIS SEQRES 8 A 308 GLY THR THR VAL GLY GLU THR VAL ALA GLY TYR MET LEU SEQRES 9 A 308 THR PHE ALA ARG ARG LEU HIS ALA TYR ARG ASP ALA GLN SEQRES 10 A 308 HIS ASP HIS ALA TRP ASP LEU PRO ARG TYR GLU GLU PRO SEQRES 11 A 308 PHE THR LEU ALA GLY GLU ARG VAL CYS VAL VAL GLY LEU SEQRES 12 A 308 GLY THR LEU GLY ARG GLY VAL VAL ASP ARG ALA ALA ALA SEQRES 13 A 308 LEU GLY MET GLU VAL VAL GLY VAL ARG ARG SER GLY ASP SEQRES 14 A 308 PRO VAL ASP ASN VAL SER THR VAL TYR THR PRO ASP ARG SEQRES 15 A 308 LEU HIS GLU ALA ILE ALA ASP ALA ARG PHE VAL VAL LEU SEQRES 16 A 308 ALA THR PRO LEU THR ASP GLU THR GLU GLY MET VAL ALA SEQRES 17 A 308 ALA PRO GLU PHE GLU THR MET ARG GLU ASP ALA SER LEU SEQRES 18 A 308 VAL ASN VAL ALA ARG GLY PRO VAL VAL VAL GLU SER ASP SEQRES 19 A 308 LEU VAL ALA ALA LEU ASP SER GLY ASP ILE ALA GLY ALA SEQRES 20 A 308 ALA LEU ASP VAL PHE SER GLU GLU PRO LEU PRO GLU ASP SEQRES 21 A 308 SER PRO LEU TRP ASP PHE GLU ASP VAL LEU ILE THR PRO SEQRES 22 A 308 HIS VAL SER ALA ALA THR SER LYS TYR HIS GLU ASP VAL SEQRES 23 A 308 ALA ALA LEU ILE ARG GLU ASN ILE GLU LYS ILE ALA THR SEQRES 24 A 308 GLY ASP GLU LEU THR ASN ARG VAL VAL SEQRES 1 B 308 MET HIS ILE GLU ARG LEU ALA VAL ASP GLU SER VAL GLY SEQRES 2 B 308 ARG ALA MET PRO PRO GLN ARG PHE ILE GLU ALA LEU SER SEQRES 3 B 308 ASP LEU GLY VAL PRO VAL GLU PHE ALA GLY GLU ASP GLU SEQRES 4 B 308 GLN PHE GLY PRO GLY ASP ALA VAL ALA SER PHE GLY HIS SEQRES 5 B 308 ARG ASP ALA PHE LEU ASP ALA ASP TRP VAL HIS CYS ILE SEQRES 6 B 308 ARG ALA GLY TYR ASP GLU PHE PRO VAL GLY VAL TYR GLU SEQRES 7 B 308 GLU ALA GLY THR TYR LEU THR ASN SER THR GLY ILE HIS SEQRES 8 B 308 GLY THR THR VAL GLY GLU THR VAL ALA GLY TYR MET LEU SEQRES 9 B 308 THR PHE ALA ARG ARG LEU HIS ALA TYR ARG ASP ALA GLN SEQRES 10 B 308 HIS ASP HIS ALA TRP ASP LEU PRO ARG TYR GLU GLU PRO SEQRES 11 B 308 PHE THR LEU ALA GLY GLU ARG VAL CYS VAL VAL GLY LEU SEQRES 12 B 308 GLY THR LEU GLY ARG GLY VAL VAL ASP ARG ALA ALA ALA SEQRES 13 B 308 LEU GLY MET GLU VAL VAL GLY VAL ARG ARG SER GLY ASP SEQRES 14 B 308 PRO VAL ASP ASN VAL SER THR VAL TYR THR PRO ASP ARG SEQRES 15 B 308 LEU HIS GLU ALA ILE ALA ASP ALA ARG PHE VAL VAL LEU SEQRES 16 B 308 ALA THR PRO LEU THR ASP GLU THR GLU GLY MET VAL ALA SEQRES 17 B 308 ALA PRO GLU PHE GLU THR MET ARG GLU ASP ALA SER LEU SEQRES 18 B 308 VAL ASN VAL ALA ARG GLY PRO VAL VAL VAL GLU SER ASP SEQRES 19 B 308 LEU VAL ALA ALA LEU ASP SER GLY ASP ILE ALA GLY ALA SEQRES 20 B 308 ALA LEU ASP VAL PHE SER GLU GLU PRO LEU PRO GLU ASP SEQRES 21 B 308 SER PRO LEU TRP ASP PHE GLU ASP VAL LEU ILE THR PRO SEQRES 22 B 308 HIS VAL SER ALA ALA THR SER LYS TYR HIS GLU ASP VAL SEQRES 23 B 308 ALA ALA LEU ILE ARG GLU ASN ILE GLU LYS ILE ALA THR SEQRES 24 B 308 GLY ASP GLU LEU THR ASN ARG VAL VAL HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET NA A 404 1 HET MG B 401 1 HET MG B 402 1 HET NA B 403 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 3 MG 5(MG 2+) FORMUL 6 NA 2(NA 1+) FORMUL 10 HOH *70(H2 O) HELIX 1 AA1 GLU A 10 GLY A 13 5 4 HELIX 2 AA2 PRO A 17 LEU A 25 1 9 HELIX 3 AA3 ARG A 53 ALA A 59 5 7 HELIX 4 AA4 PRO A 73 GLY A 81 1 9 HELIX 5 AA5 HIS A 91 ARG A 109 1 19 HELIX 6 AA6 ARG A 109 ASP A 119 1 11 HELIX 7 AA7 GLY A 144 LEU A 157 1 14 HELIX 8 AA8 THR A 179 ASP A 181 5 3 HELIX 9 AA9 ARG A 182 ALA A 188 1 7 HELIX 10 AB1 ALA A 208 MET A 215 1 8 HELIX 11 AB2 ARG A 226 VAL A 230 5 5 HELIX 12 AB3 VAL A 231 SER A 241 1 11 HELIX 13 AB4 SER A 261 PHE A 266 5 6 HELIX 14 AB5 LYS A 281 THR A 299 1 19 HELIX 15 AB6 SER B 11 ALA B 15 5 5 HELIX 16 AB7 PRO B 17 SER B 26 1 10 HELIX 17 AB8 ARG B 53 ALA B 59 5 7 HELIX 18 AB9 PRO B 73 GLY B 81 1 9 HELIX 19 AC1 HIS B 91 ARG B 109 1 19 HELIX 20 AC2 ARG B 109 ASP B 119 1 11 HELIX 21 AC3 GLY B 144 LEU B 157 1 14 HELIX 22 AC4 THR B 179 ASP B 181 5 3 HELIX 23 AC5 ARG B 182 ASP B 189 1 8 HELIX 24 AC6 ALA B 208 MET B 215 1 8 HELIX 25 AC7 ARG B 226 VAL B 230 5 5 HELIX 26 AC8 VAL B 231 SER B 241 1 11 HELIX 27 AC9 SER B 261 PHE B 266 5 6 HELIX 28 AD1 LYS B 281 GLY B 300 1 20 SHEET 1 AA1 5 VAL A 32 PHE A 34 0 SHEET 2 AA1 5 ARG A 5 VAL A 8 1 N LEU A 6 O GLU A 33 SHEET 3 AA1 5 ASP A 45 SER A 49 1 O ALA A 46 N ALA A 7 SHEET 4 AA1 5 TRP A 61 CYS A 64 1 O TRP A 61 N VAL A 47 SHEET 5 AA1 5 TYR A 83 THR A 85 1 O THR A 85 N CYS A 64 SHEET 1 AA2 7 THR A 176 TYR A 178 0 SHEET 2 AA2 7 GLU A 160 VAL A 164 1 N GLY A 163 O TYR A 178 SHEET 3 AA2 7 ARG A 137 VAL A 141 1 N VAL A 138 O GLU A 160 SHEET 4 AA2 7 PHE A 192 LEU A 195 1 O VAL A 194 N VAL A 141 SHEET 5 AA2 7 SER A 220 ASN A 223 1 O VAL A 222 N VAL A 193 SHEET 6 AA2 7 GLY A 246 LEU A 249 1 O ALA A 248 N ASN A 223 SHEET 7 AA2 7 VAL A 269 ILE A 271 1 O LEU A 270 N LEU A 249 SHEET 1 AA3 5 VAL B 32 ALA B 35 0 SHEET 2 AA3 5 ARG B 5 ASP B 9 1 N VAL B 8 O ALA B 35 SHEET 3 AA3 5 ASP B 45 SER B 49 1 O ALA B 46 N ALA B 7 SHEET 4 AA3 5 TRP B 61 CYS B 64 1 O TRP B 61 N VAL B 47 SHEET 5 AA3 5 TYR B 83 THR B 85 1 O THR B 85 N CYS B 64 SHEET 1 AA4 7 THR B 176 TYR B 178 0 SHEET 2 AA4 7 GLU B 160 VAL B 164 1 N GLY B 163 O TYR B 178 SHEET 3 AA4 7 ARG B 137 VAL B 141 1 N VAL B 138 O GLU B 160 SHEET 4 AA4 7 PHE B 192 LEU B 195 1 O VAL B 194 N VAL B 141 SHEET 5 AA4 7 SER B 220 ASN B 223 1 O VAL B 222 N LEU B 195 SHEET 6 AA4 7 GLY B 246 LEU B 249 1 O ALA B 248 N LEU B 221 SHEET 7 AA4 7 VAL B 269 ILE B 271 1 O LEU B 270 N LEU B 249 LINK OE2 GLU A 211 MG MG A 401 1555 1555 2.19 LINK O PHE A 212 NA NA A 404 1555 1555 2.36 LINK O GLU A 213 NA NA A 404 1555 1555 2.77 LINK O MET A 215 NA NA A 404 1555 1555 2.38 LINK O ASP A 243 NA NA A 404 1555 1555 2.28 LINK OD1 ASP A 265 MG MG A 403 1555 1555 2.21 LINK MG MG A 401 O HOH A 509 1555 1555 1.84 LINK MG MG A 401 O HOH A 524 1555 1555 2.07 LINK MG MG A 401 O HOH B 503 1555 1655 1.89 LINK MG MG A 401 O HOH B 512 1555 1655 1.90 LINK MG MG A 401 O HOH B 534 1555 1655 2.06 LINK MG MG A 402 OD1 ASP B 265 1555 1555 2.41 LINK O HOH A 501 MG MG B 402 2556 1555 2.04 LINK O HOH A 502 MG MG B 402 2556 1555 2.30 LINK O HOH A 503 MG MG B 402 2556 1555 2.38 LINK O HOH A 508 MG MG B 402 2556 1555 2.19 LINK O HOH A 510 MG MG B 401 1455 1555 2.15 LINK O HOH A 517 MG MG B 401 1455 1555 2.00 LINK O HOH A 529 MG MG B 401 1455 1555 2.20 LINK OE2 GLU B 211 MG MG B 401 1555 1555 2.28 LINK O PHE B 212 NA NA B 403 1555 1555 2.32 LINK O GLU B 213 NA NA B 403 1555 1555 2.85 LINK O MET B 215 NA NA B 403 1555 1555 2.12 LINK O ASP B 243 NA NA B 403 1555 1555 2.39 LINK MG MG B 401 O HOH B 505 1555 1555 1.93 LINK MG MG B 401 O HOH B 509 1555 1555 2.06 LINK MG MG B 402 O HOH B 502 1555 1555 1.98 LINK MG MG B 402 O HOH B 535 1555 1555 2.04 LINK NA NA B 403 O HOH B 517 1555 1555 2.44 CISPEP 1 GLU A 255 PRO A 256 0 -12.01 CISPEP 2 GLU B 255 PRO B 256 0 -7.15 CRYST1 62.352 75.986 74.589 90.00 93.99 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 0.016038 0.000000 0.001119 0.00000 SCALE2 0.000000 0.013160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013439 0.00000 CONECT 1612 4705 CONECT 1616 4708 CONECT 1627 4708 CONECT 1643 4708 CONECT 1842 4708 CONECT 2012 4707 CONECT 3964 4709 CONECT 3968 4711 CONECT 3979 4711 CONECT 3995 4711 CONECT 4194 4711 CONECT 4366 4706 CONECT 4705 1612 4720 4735 CONECT 4706 4366 CONECT 4707 2012 CONECT 4708 1616 1627 1643 1842 CONECT 4709 3964 4746 4750 CONECT 4710 4743 4776 CONECT 4711 3968 3979 3995 4194 CONECT 4711 4758 CONECT 4720 4705 CONECT 4735 4705 CONECT 4743 4710 CONECT 4746 4709 CONECT 4750 4709 CONECT 4758 4711 CONECT 4776 4710 MASTER 426 0 7 28 24 0 0 6 4775 2 27 48 END