HEADER OXIDOREDUCTASE 28-JAN-25 9I5F TITLE GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A (GAPDHA) NAD HOLOENZYME, TITLE 2 FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAP); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI 26695; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 GENE: HP_1346; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETE151/D KEYWDS HOLOENZYME, GLYCOLYSIS, GLUCONEOGENESIS, CARBOHYDRATE METABOLISM, KEYWDS 2 ROSSMANN FOLD, HELICOBACTER PYLORI, NUCLEOTIDE BINDING DOMAIN, KEYWDS 3 OXIDOREDUCTASE, NICOTINAMIDE ADENINE DINUCLEOTIDE EXPDTA X-RAY DIFFRACTION AUTHOR S.P.FOSTER,P.C.E.MOODY REVDAT 1 18-FEB-26 9I5F 0 JRNL AUTH S.P.FOSTER,P.C.E.MOODY JRNL TITL GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENAE A (GAPDHA) NAD JRNL TITL 2 HOLOENZYME, FROM HELICOBACTER PYLORI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.16 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 61.3 REMARK 3 NUMBER OF REFLECTIONS : 82089 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) : 0.136 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.109 REMARK 3 FREE R VALUE TEST SET COUNT : 4194 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 390 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 4.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2534 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.00300 REMARK 3 B22 (A**2) : 2.15400 REMARK 3 B33 (A**2) : -0.15100 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): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.950 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2766 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2678 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3787 ; 1.989 ; 1.808 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6191 ; 0.843 ; 1.763 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 7.122 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 9.620 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;11.376 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 462 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3193 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 590 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 495 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 190 ; 0.150 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1299 ; 0.164 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 205 ; 0.143 ; 0.200 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): 1364 ; 3.557 ; 1.183 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1364 ; 3.520 ; 1.183 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1716 ; 5.195 ; 2.135 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1717 ; 5.202 ; 2.137 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1402 ; 5.946 ; 1.465 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1391 ; 5.727 ; 1.453 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2056 ; 8.327 ; 2.574 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2039 ; 8.178 ; 2.546 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): 5444 ; 4.950 ; 3.000 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 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 9I5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1292139438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-23 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6888 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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 67.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.4 REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM SODIUM CITRATE TRIBASIC 20% PEG REMARK 280 3350 (W/V) SOLUTION WAS MIXED 4:1:1 OR 3:2:1 (PROTEIN: RESERVOIR: REMARK 280 SEEDS) IN 300NL DROPS., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 42.96800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.43300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.85050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.96800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.43300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.85050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.96800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.43300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.85050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.96800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.43300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 47.85050 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: TETRAMERIC 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 -1.000000 0.000000 0.000000 -85.93600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 -85.93600 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 525 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 777 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 799 LIES ON A SPECIAL POSITION. 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 HD1 HIS A 189 H ASP A 191 1.22 REMARK 500 OE2 GLU A 39 O HOH A 502 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 91 CD GLU A 91 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 GLU A 91 CG - CD - OE1 ANGL. DEV. = -16.1 DEGREES REMARK 500 GLU A 91 CG - CD - OE2 ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU A 184 CB - CG - CD1 ANGL. DEV. = 16.0 DEGREES REMARK 500 LYS A 259 CB - CG - CD ANGL. DEV. = 20.3 DEGREES REMARK 500 LYS A 259 CD - CE - NZ ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 276 NE - CZ - NH1 ANGL. DEV. = -3.8 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 71 58.09 -149.08 REMARK 500 SER A 76 79.46 -150.69 REMARK 500 ASN A 112 -132.11 57.58 REMARK 500 SER A 120 36.40 -79.43 REMARK 500 VAL A 133 -60.78 -105.30 REMARK 500 ALA A 147 -161.60 62.50 REMARK 500 LYS A 166 99.84 70.57 REMARK 500 THR A 205 -167.54 -166.66 REMARK 500 VAL A 236 131.77 85.37 REMARK 500 HIS A 264 -100.55 -121.16 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 818 DISTANCE = 6.47 ANGSTROMS 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 NA A 409 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 109 O REMARK 620 2 HOH A 687 O 107.2 REMARK 620 3 HOH A 705 O 121.2 121.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 178 OH REMARK 620 2 LEU A 184 O 99.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 408 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 260 OD2 REMARK 620 2 HOH A 600 O 107.0 REMARK 620 3 HOH A 755 O 120.3 126.3 REMARK 620 4 HOH A 796 O 102.9 92.6 99.8 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9FOD RELATED DB: PDB REMARK 900 9FOD CONTAINS THE SAME PROTEIN AS AN APOENZYME REMARK 900 RELATED ID: 9FQ4 RELATED DB: PDB REMARK 900 9FQ4 CONTAINS THE SAME PROTEIN AS THE NADP HOLOENZYME DBREF 9I5F A 1 330 UNP O25902 O25902_HELPY 1 330 SEQRES 1 A 330 MET PRO ILE ARG ILE ALA ILE ASN GLY THR GLY ARG ILE SEQRES 2 A 330 GLY LEU CYS ALA ILE ARG VAL ALA SER GLN ARG LYS ASP SEQRES 3 A 330 ILE GLU ILE VAL ALA ILE ASN SER THR ALA GLU LEU GLU SEQRES 4 A 330 THR LEU LEU HIS LEU ILE ARG HIS ASP SER VAL HIS GLY SEQRES 5 A 330 HIS PHE GLU ALA GLN LEU ASN ALA ASP ARG THR LEU ASN SEQRES 6 A 330 ILE GLY HIS SER LYS ASN ILE LEU VAL LEU SER GLU ARG SEQRES 7 A 330 ASP ILE ASN LYS LEU ASP PHE SER ALA ALA ASN ALA GLU SEQRES 8 A 330 ILE ILE ILE GLU CYS THR GLY LYS PHE ASN SER LEU GLU SEQRES 9 A 330 ALA SER SER ALA HIS LEU LYS ASN SER VAL LYS LYS VAL SEQRES 10 A 330 ILE ILE SER ALA PRO ALA GLN ASN THR PRO THR PHE VAL SEQRES 11 A 330 TYR GLY VAL ASN HIS LYS ASN TYR HIS ASN GLU SER VAL SEQRES 12 A 330 ILE SER ASN ALA SER CSD THR THR ASN ALA SER ALA PRO SEQRES 13 A 330 LEU LEU LYS ILE LEU ASP GLU ALA PHE LYS VAL GLU ASN SEQRES 14 A 330 ALA LEU LEU THR THR ILE HIS SER TYR THR ASN ASP GLN SEQRES 15 A 330 ASN LEU LEU ASP THR LYS HIS LYS ASP ILE ARG ARG ALA SEQRES 16 A 330 ARG ALA ALA GLY LEU ASN LEU ILE PRO THR SER THR GLY SEQRES 17 A 330 VAL SER LYS ALA ILE SER LEU VAL LEU PRO HIS LEU GLY SEQRES 18 A 330 PRO LYS VAL THR GLY LEU ALA ILE ARG VAL PRO THR PRO SEQRES 19 A 330 ASN VAL SER LEU VAL ASP LEU SER LEU ASN PHE LYS LYS SEQRES 20 A 330 SER VAL SER LYS ALA SER VAL GLN HIS ALA LEU LYS ASP SEQRES 21 A 330 ALA CYS LYS HIS ALA PHE LYS GLY VAL VAL SER ILE ASP SEQRES 22 A 330 GLU GLU ARG LEU VAL SER SER ASP PHE ILE SER SER PRO SEQRES 23 A 330 PHE SER ALA ILE VAL ILE ASP ASP GLN ILE MET THR ILE SEQRES 24 A 330 GLY GLU LYS ASN ALA LYS VAL LEU ALA TRP TYR ASP ASN SEQRES 25 A 330 GLU MET GLY TYR SER GLU ARG LEU ILE ASP MET ALA GLN SEQRES 26 A 330 TYR ILE ALA GLN ASN MODRES 9I5F CSD A 149 CYS MODIFIED RESIDUE HET CSD A 149 13 HET SO4 A 401 10 HET EOH A 402 9 HET NAD A 403 70 HET ART A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET NA A 407 1 HET NA A 408 1 HET NA A 409 1 HETNAM CSD 3-SULFINOALANINE HETNAM SO4 SULFATE ION HETNAM EOH ETHANOL HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM ART ARSENATE HETNAM NA SODIUM ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 SO4 3(O4 S 2-) FORMUL 3 EOH C2 H6 O FORMUL 4 NAD C21 H27 N7 O14 P2 FORMUL 5 ART AS O4 3- FORMUL 8 NA 3(NA 1+) FORMUL 11 HOH *318(H2 O) HELIX 1 AA1 GLY A 11 GLN A 23 1 13 HELIX 2 AA2 GLU A 37 ARG A 46 1 10 HELIX 3 AA3 PHE A 85 ASN A 89 5 5 HELIX 4 AA4 SER A 102 SER A 107 1 6 HELIX 5 AA5 ALA A 108 LEU A 110 5 3 HELIX 6 AA6 ASN A 134 TYR A 138 5 5 HELIX 7 AA7 SER A 148 LYS A 166 1 19 HELIX 8 AA8 GLY A 208 LEU A 217 1 10 HELIX 9 AA9 LEU A 220 PRO A 222 5 3 HELIX 10 AB1 SER A 250 HIS A 264 1 15 HELIX 11 AB2 VAL A 278 ILE A 283 5 6 HELIX 12 AB3 ASP A 294 ILE A 296 5 3 HELIX 13 AB4 GLU A 313 ASN A 330 1 18 SHEET 1 AA1 8 GLN A 57 LEU A 58 0 SHEET 2 AA1 8 LEU A 64 ILE A 66 -1 O ASN A 65 N GLN A 57 SHEET 3 AA1 8 SER A 69 LEU A 75 -1 O SER A 69 N ILE A 66 SHEET 4 AA1 8 ILE A 27 ASN A 33 1 N ILE A 32 O LEU A 75 SHEET 5 AA1 8 ILE A 3 ASN A 8 1 N ILE A 3 O GLU A 28 SHEET 6 AA1 8 ILE A 92 GLU A 95 1 O ILE A 94 N ALA A 6 SHEET 7 AA1 8 LYS A 116 ILE A 119 1 O ILE A 118 N ILE A 93 SHEET 8 AA1 8 VAL A 143 SER A 145 1 O ILE A 144 N ILE A 119 SHEET 1 AA2 2 HIS A 47 ASP A 48 0 SHEET 2 AA2 2 GLY A 52 HIS A 53 -1 O GLY A 52 N ASP A 48 SHEET 1 AA3 7 ILE A 203 THR A 205 0 SHEET 2 AA3 7 VAL A 224 VAL A 231 -1 O ALA A 228 N THR A 205 SHEET 3 AA3 7 VAL A 167 SER A 177 1 N THR A 174 O ILE A 229 SHEET 4 AA3 7 SER A 237 PHE A 245 -1 O LEU A 238 N ILE A 175 SHEET 5 AA3 7 ASN A 303 TYR A 310 -1 O ALA A 304 N LEU A 243 SHEET 6 AA3 7 ALA A 289 ILE A 292 -1 N ILE A 292 O LEU A 307 SHEET 7 AA3 7 VAL A 270 ASP A 273 1 N ASP A 273 O VAL A 291 SHEET 1 AA4 6 ILE A 203 THR A 205 0 SHEET 2 AA4 6 VAL A 224 VAL A 231 -1 O ALA A 228 N THR A 205 SHEET 3 AA4 6 VAL A 167 SER A 177 1 N THR A 174 O ILE A 229 SHEET 4 AA4 6 SER A 237 PHE A 245 -1 O LEU A 238 N ILE A 175 SHEET 5 AA4 6 ASN A 303 TYR A 310 -1 O ALA A 304 N LEU A 243 SHEET 6 AA4 6 MET A 297 ILE A 299 -1 N MET A 297 O LYS A 305 LINK C SER A 148 N CSD A 149 1555 1555 1.34 LINK C CSD A 149 N THR A 150 1555 1555 1.34 LINK O HIS A 109 NA NA A 409 1555 1555 2.83 LINK OH TYR A 178 NA NA A 407 1555 2455 2.88 LINK O LEU A 184 NA NA A 407 1555 1555 2.67 LINK OD2AASP A 260 NA NA A 408 1555 1555 2.77 LINK NA NA A 408 O HOH A 600 1555 1555 2.74 LINK NA NA A 408 O HOH A 755 1555 1555 2.68 LINK NA NA A 408 O HOH A 796 1555 1555 2.79 LINK NA NA A 409 O HOH A 687 1555 1555 2.82 LINK NA NA A 409 O HOH A 705 1555 1555 2.80 CRYST1 85.936 94.866 95.701 90.00 90.00 90.00 I 2 2 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 0.011637 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010449 0.00000 CONECT 1727 5489 CONECT 2339 2348 CONECT 2348 2339 2349 2356 CONECT 2349 2348 2350 2352 2357 CONECT 2350 2349 2351 2358 2359 CONECT 2351 2350 2354 2355 CONECT 2352 2349 2353 2361 CONECT 2353 2352 CONECT 2354 2351 CONECT 2355 2351 2360 CONECT 2356 2348 CONECT 2357 2349 CONECT 2358 2350 CONECT 2359 2350 CONECT 2360 2355 CONECT 2361 2352 CONECT 2936 5487 CONECT 4278 5488 CONECT 5383 5385 5387 5389 5391 CONECT 5384 5386 5388 5390 5392 CONECT 5385 5383 CONECT 5386 5384 CONECT 5387 5383 CONECT 5388 5384 CONECT 5389 5383 CONECT 5390 5384 CONECT 5391 5383 CONECT 5392 5384 CONECT 5393 5394 5395 5396 5397 CONECT 5394 5393 5398 5399 5400 CONECT 5395 5393 5401 CONECT 5396 5393 CONECT 5397 5393 CONECT 5398 5394 CONECT 5399 5394 CONECT 5400 5394 CONECT 5401 5395 CONECT 5402 5403 5404 5405 5424 CONECT 5403 5402 CONECT 5404 5402 CONECT 5405 5402 5406 CONECT 5406 5405 5407 5446 5447 CONECT 5407 5406 5408 5409 5448 CONECT 5408 5407 5413 CONECT 5409 5407 5410 5411 5449 CONECT 5410 5409 5450 CONECT 5411 5409 5412 5413 5451 CONECT 5412 5411 5452 CONECT 5413 5408 5411 5414 5453 CONECT 5414 5413 5415 5423 CONECT 5415 5414 5416 5454 CONECT 5416 5415 5417 CONECT 5417 5416 5418 5423 CONECT 5418 5417 5419 5420 CONECT 5419 5418 5455 5456 CONECT 5420 5418 5421 CONECT 5421 5420 5422 5457 CONECT 5422 5421 5423 CONECT 5423 5414 5417 5422 CONECT 5424 5402 5425 CONECT 5425 5424 5426 5427 5428 CONECT 5426 5425 CONECT 5427 5425 CONECT 5428 5425 5429 CONECT 5429 5428 5430 5458 5459 CONECT 5430 5429 5431 5432 5460 CONECT 5431 5430 5436 CONECT 5432 5430 5433 5434 5461 CONECT 5433 5432 5462 CONECT 5434 5432 5435 5436 5463 CONECT 5435 5434 5464 CONECT 5436 5431 5434 5437 5465 CONECT 5437 5436 5438 5445 CONECT 5438 5437 5439 5466 CONECT 5439 5438 5440 5443 CONECT 5440 5439 5441 5442 CONECT 5441 5440 CONECT 5442 5440 5467 5468 CONECT 5443 5439 5444 5469 CONECT 5444 5443 5445 5470 CONECT 5445 5437 5444 5471 CONECT 5446 5406 CONECT 5447 5406 CONECT 5448 5407 CONECT 5449 5409 CONECT 5450 5410 CONECT 5451 5411 CONECT 5452 5412 CONECT 5453 5413 CONECT 5454 5415 CONECT 5455 5419 CONECT 5456 5419 CONECT 5457 5421 CONECT 5458 5429 CONECT 5459 5429 CONECT 5460 5430 CONECT 5461 5432 CONECT 5462 5433 CONECT 5463 5434 CONECT 5464 5435 CONECT 5465 5436 CONECT 5466 5438 CONECT 5467 5442 CONECT 5468 5442 CONECT 5469 5443 CONECT 5470 5444 CONECT 5471 5445 CONECT 5472 5473 5474 5475 5476 CONECT 5473 5472 CONECT 5474 5472 CONECT 5475 5472 CONECT 5476 5472 CONECT 5477 5478 5479 5480 5481 CONECT 5478 5477 CONECT 5479 5477 CONECT 5480 5477 CONECT 5481 5477 CONECT 5482 5483 5484 5485 5486 CONECT 5483 5482 CONECT 5484 5482 CONECT 5485 5482 CONECT 5486 5482 CONECT 5487 2936 CONECT 5488 4278 5589 5744 5785 CONECT 5489 1727 5676 5694 CONECT 5589 5488 CONECT 5676 5489 CONECT 5694 5489 CONECT 5744 5488 CONECT 5785 5488 MASTER 399 0 10 13 23 0 0 6 2922 1 130 26 END