HEADER HYDROLASE 25-APR-12 4ARO TITLE HAFNIA ALVEI PHYTASE IN COMPLEX WITH MYO-INOSITOL HEXAKIS SULPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE ACID PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 34-446; COMPND 5 SYNONYM: PHYTASE; COMPND 6 EC: 3.1.3.26; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAFNIA ALVEI; SOURCE 3 ORGANISM_TAXID: 569; SOURCE 4 EXPRESSION_SYSTEM: ASPERGILLUS ORYZAE; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 5062 KEYWDS HYDROLASE, 6-PHYTASE, MYO-INOSITOL HEXAKIS PHOSPHATE KEYWDS 2 PHOSPHOHYDROLASE, HAPP EXPDTA X-RAY DIFFRACTION AUTHOR O.V.MOROZ,E.B.BLAGOVA,A.ARIZA,J.P.TURKENBURG,J.VEVODOVA,S.ROBERTS, AUTHOR 2 J.VIND,C.SJOHOLM,S.F.LASSEN,L.DE MARIA,V.GLITSOE,L.K.SKOV,K.S.WILSON REVDAT 7 20-NOV-24 4ARO 1 REMARK REVDAT 6 20-DEC-23 4ARO 1 REMARK REVDAT 5 21-JUN-17 4ARO 1 LINK REVDAT 4 05-FEB-14 4ARO 1 JRNL REVDAT 3 07-AUG-13 4ARO 1 HETATM REVDAT 2 19-JUN-13 4ARO 1 JRNL REVDAT 1 08-MAY-13 4ARO 0 JRNL AUTH A.ARIZA,O.V.MOROZ,E.V.BLAGOVA,J.P.TURKENBURG,J.WATERMAN, JRNL AUTH 2 S.M.ROBERTS,J.VIND,C.SJOHOLM,S.F.LASSEN,L.DE MARIA, JRNL AUTH 3 V.GLITSOE,L.K.SKOV,K.S.WILSON JRNL TITL DEGRADATION OF PHYTATE BY THE 6-PHYTASE FROM HAFNIA ALVEI: A JRNL TITL 2 COMBINED STRUCTURAL AND SOLUTION STUDY. JRNL REF PLOS ONE V. 8 65062 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23741456 JRNL DOI 10.1371/JOURNAL.PONE.0065062 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 51816 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) : 0.156 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2772 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) : 1.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3759 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.89000 REMARK 3 B12 (A**2) : 0.28000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.858 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3372 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3106 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4657 ; 1.870 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7174 ; 0.887 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 435 ; 5.886 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;35.207 ;24.964 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;13.531 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;16.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 527 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3849 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 747 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 24 REMARK 3 RESIDUE RANGE : A 46 A 136 REMARK 3 RESIDUE RANGE : A 265 A 413 REMARK 3 ORIGIN FOR THE GROUP (A): -33.4720 10.6812 -3.6742 REMARK 3 T TENSOR REMARK 3 T11: 0.0126 T22: 0.0448 REMARK 3 T33: 0.0234 T12: 0.0055 REMARK 3 T13: 0.0119 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.7701 L22: 0.8696 REMARK 3 L33: 1.2016 L12: 0.0587 REMARK 3 L13: -0.6750 L23: 0.0694 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: -0.1126 S13: 0.0891 REMARK 3 S21: 0.0876 S22: -0.0233 S23: 0.1268 REMARK 3 S31: -0.0388 S32: -0.1451 S33: 0.0120 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 45 REMARK 3 RESIDUE RANGE : A 137 A 264 REMARK 3 ORIGIN FOR THE GROUP (A): -17.7302 -7.4971 -15.2673 REMARK 3 T TENSOR REMARK 3 T11: 0.0825 T22: 0.0358 REMARK 3 T33: 0.0626 T12: 0.0258 REMARK 3 T13: 0.0197 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.3721 L22: 1.4107 REMARK 3 L33: 0.9223 L12: -0.1945 REMARK 3 L13: -0.4669 L23: 0.2287 REMARK 3 S TENSOR REMARK 3 S11: -0.0872 S12: -0.1264 S13: -0.2831 REMARK 3 S21: 0.1373 S22: -0.0234 S23: -0.0019 REMARK 3 S31: 0.2654 S32: 0.1089 S33: 0.1106 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 HYDROGENS HAVE REMARK 3 BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4ARO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-12. REMARK 100 THE DEPOSITION ID IS D_1290052219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54630 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 41.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 4ARS REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MG/ML PROTEIN IN 50MM SODIUM ACETATE REMARK 280 PH 4.5 WITH 5 MM MIHS IN 50 MM SODIUM ACETATE PH 4.5 IN JCSG REMARK 280 CONDITION 12 0.04 M KH2PO4 16% PEG 8K 20% GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.08000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.54000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.54000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.08000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 748 LIES ON A SPECIAL POSITION. 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 SER A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 ASP A 77 REMARK 465 ASN A 78 REMARK 465 ASN A 184 REMARK 465 ILE A 185 REMARK 465 GLY A 186 REMARK 465 LYS A 187 REMARK 465 ASN A 202 REMARK 465 ASP A 203 REMARK 465 ASP A 204 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 9 CD OE1 NE2 REMARK 470 ARG A 65 NE CZ NH1 NH2 REMARK 470 ARG A 67 CZ NH1 NH2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 LYS A 139 CD CE NZ REMARK 470 GLU A 155 CD OE1 OE2 REMARK 470 ARG A 160 NH2 REMARK 470 ARG A 198 CZ NH1 NH2 REMARK 470 ASN A 206 CG OD1 ND2 REMARK 470 LYS A 207 CG CD CE NZ REMARK 470 LYS A 234 CD CE NZ REMARK 470 LYS A 268 NZ REMARK 470 ASP A 293 OD2 REMARK 470 ARG A 400 CG CD NE CZ NH1 NH2 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 660 O HOH A 937 1.95 REMARK 500 O HOH A 665 O HOH A 768 2.02 REMARK 500 O LYS A 76 O HOH A 601 2.02 REMARK 500 O HOH A 630 O HOH A 691 2.06 REMARK 500 C ILE A 201 O HOH A 628 2.12 REMARK 500 OD1 ASN A 344 O HOH A 603 2.12 REMARK 500 O HOH A 747 O HOH A 829 2.15 REMARK 500 O HOH A 964 O HOH A 1004 2.16 REMARK 500 OH TYR A 64 O HOH A 604 2.16 REMARK 500 O HOH A 850 O HOH A 874 2.17 REMARK 500 O HOH A 831 O HOH A 934 2.17 REMARK 500 O HOH A 864 O HOH A 970 2.17 REMARK 500 CB ASN A 206 O HOH A 786 2.19 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 1009 O HOH A 1009 5554 1.84 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 222 CD GLU A 222 OE1 0.071 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 ASP A 307 CB - CG - OD1 ANGL. DEV. = 6.4 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 THR A 263 118.42 -38.99 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 A1009 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A1010 DISTANCE = 6.01 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 K A 504 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 230 O REMARK 620 2 GLY A 231 O 77.5 REMARK 620 3 IHS A 502 O1 104.4 141.2 REMARK 620 4 IHS A 502 O4 83.7 91.7 51.0 REMARK 620 5 IHS A 502 O13 105.3 158.9 59.2 109.4 REMARK 620 6 IHS A 502 O15 157.4 124.0 55.2 88.5 57.7 REMARK 620 7 IHS A 502 O35 153.2 76.1 93.6 92.9 100.9 48.0 REMARK 620 8 IHS A 502 O43 85.8 111.5 107.3 151.7 48.9 91.3 107.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHS A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHS A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ARS RELATED DB: PDB REMARK 900 HAFNIA ALVEI PHYTASE APO FORM REMARK 900 RELATED ID: 4ARU RELATED DB: PDB REMARK 900 HAFNIA ALVEI PHYTASE IN COMPLEX WITH TARTRATE REMARK 900 RELATED ID: 4ARV RELATED DB: PDB REMARK 900 YERSINIA KRISTENSENII PHYTASE APO FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 EUROPEAN NUCLEOTIDE ARCHIVE ENTRY JQ394762 DBREF 4ARO A 1 413 UNP G9Y2J2 G9Y2J2_HAFAL 34 446 SEQADV 4ARO ALA A 308 UNP H9TUK5 THR 341 ENGINEERED MUTATION SEQRES 1 A 413 SER ASP THR ALA PRO ALA GLY PHE GLN LEU GLU LYS VAL SEQRES 2 A 413 VAL ILE LEU SER ARG HIS GLY VAL ARG ALA PRO THR LYS SEQRES 3 A 413 MET THR GLN THR MET ARG ASP VAL THR PRO HIS GLN TRP SEQRES 4 A 413 PRO GLU TRP PRO VAL LYS LEU GLY TYR ILE THR PRO ARG SEQRES 5 A 413 GLY GLU HIS LEU ILE SER LEU MET GLY GLY PHE TYR ARG SEQRES 6 A 413 GLU ARG PHE GLN GLN GLN GLY LEU LEU PRO LYS ASP ASN SEQRES 7 A 413 CYS PRO THR PRO ASP ALA VAL TYR VAL TRP ALA ASP VAL SEQRES 8 A 413 ASP GLN ARG THR ARG LYS THR GLY GLU ALA PHE LEU ALA SEQRES 9 A 413 GLY LEU ALA PRO GLN CYS ASP LEU ALA ILE HIS HIS GLN SEQRES 10 A 413 GLN ASN THR GLN GLN ALA ASP PRO LEU PHE HIS PRO VAL SEQRES 11 A 413 LYS ALA GLY ILE CYS SER MET ASP LYS SER GLN VAL HIS SEQRES 12 A 413 ALA ALA VAL GLU LYS GLN ALA GLY THR PRO ILE GLU THR SEQRES 13 A 413 LEU ASN GLN ARG TYR GLN ALA SER LEU ALA LEU MET SER SEQRES 14 A 413 SER VAL LEU ASP PHE PRO LYS SER PRO TYR CYS GLN GLN SEQRES 15 A 413 HIS ASN ILE GLY LYS LEU CYS ASP PHE SER GLN ALA MET SEQRES 16 A 413 PRO SER ARG LEU ALA ILE ASN ASP ASP GLY ASN LYS VAL SEQRES 17 A 413 ALA LEU GLU GLY ALA VAL GLY LEU ALA SER THR LEU ALA SEQRES 18 A 413 GLU ILE PHE LEU LEU GLU HIS ALA GLN GLY MET PRO LYS SEQRES 19 A 413 VAL ALA TRP GLY ASN ILE HIS THR GLU GLN GLN TRP ASN SEQRES 20 A 413 SER LEU LEU LYS LEU HIS ASN ALA GLN PHE ASP LEU MET SEQRES 21 A 413 SER ARG THR PRO TYR ILE ALA LYS HIS ASN GLY THR PRO SEQRES 22 A 413 LEU LEU GLN THR ILE ALA HIS ALA LEU GLY SER ASN ILE SEQRES 23 A 413 THR SER ARG PRO LEU PRO ASP ILE SER PRO ASP ASN LYS SEQRES 24 A 413 ILE LEU PHE ILE ALA GLY HIS ASP ALA ASN ILE ALA ASN SEQRES 25 A 413 ILE SER GLY MET LEU GLY MET THR TRP THR LEU PRO GLY SEQRES 26 A 413 GLN PRO ASP ASN THR PRO PRO GLY GLY ALA LEU VAL PHE SEQRES 27 A 413 GLU ARG TRP VAL ASP ASN ALA GLY LYS PRO TYR VAL SER SEQRES 28 A 413 VAL ASN MET VAL TYR GLN THR LEU ALA GLN LEU HIS ASP SEQRES 29 A 413 GLN ALA PRO LEU THR LEU GLN HIS PRO ALA GLY SER VAL SEQRES 30 A 413 ARG LEU ASN ILE PRO GLY CYS SER ASP GLN THR PRO ASP SEQRES 31 A 413 GLY TYR CYS PRO LEU SER THR PHE SER ARG LEU VAL SER SEQRES 32 A 413 HIS SER VAL GLU PRO ALA CYS GLN LEU PRO HET IHS A 501 36 HET IHS A 502 36 HET PEG A 503 7 HET K A 504 1 HETNAM IHS D-MYO-INOSITOL-HEXASULPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM K POTASSIUM ION FORMUL 2 IHS 2(C6 H12 O24 S6) FORMUL 4 PEG C4 H10 O3 FORMUL 5 K K 1+ FORMUL 6 HOH *410(H2 O) HELIX 1 AA1 THR A 28 VAL A 34 1 7 HELIX 2 AA2 THR A 50 GLN A 71 1 22 HELIX 3 AA3 THR A 81 ASP A 83 5 3 HELIX 4 AA4 ASP A 92 ALA A 107 1 16 HELIX 5 AA5 ASP A 138 GLY A 151 1 14 HELIX 6 AA6 PRO A 153 GLU A 155 5 3 HELIX 7 AA7 THR A 156 TYR A 161 1 6 HELIX 8 AA8 TYR A 161 ASP A 173 1 13 HELIX 9 AA9 PHE A 174 LYS A 176 5 3 HELIX 10 AB1 SER A 177 HIS A 183 1 7 HELIX 11 AB2 ASP A 190 MET A 195 1 6 HELIX 12 AB3 GLY A 212 GLN A 230 1 19 HELIX 13 AB4 VAL A 235 ASN A 239 5 5 HELIX 14 AB5 THR A 242 SER A 261 1 20 HELIX 15 AB6 THR A 263 GLY A 283 1 21 HELIX 16 AB7 HIS A 306 GLY A 318 1 13 HELIX 17 AB8 THR A 358 GLN A 365 1 8 HELIX 18 AB9 LEU A 395 VAL A 406 1 12 HELIX 19 AC1 GLU A 407 GLN A 411 5 5 SHEET 1 AA1 7 HIS A 115 HIS A 116 0 SHEET 2 AA1 7 VAL A 85 ALA A 89 1 N ALA A 89 O HIS A 115 SHEET 3 AA1 7 ILE A 300 GLY A 305 1 O PHE A 302 N TYR A 86 SHEET 4 AA1 7 GLN A 9 ARG A 18 1 N ILE A 15 O ILE A 303 SHEET 5 AA1 7 ALA A 335 VAL A 342 -1 O PHE A 338 N VAL A 14 SHEET 6 AA1 7 PRO A 348 TYR A 356 -1 O TYR A 349 N TRP A 341 SHEET 7 AA1 7 GLY A 375 ARG A 378 -1 O VAL A 377 N MET A 354 SHEET 1 AA2 7 HIS A 115 HIS A 116 0 SHEET 2 AA2 7 VAL A 85 ALA A 89 1 N ALA A 89 O HIS A 115 SHEET 3 AA2 7 ILE A 300 GLY A 305 1 O PHE A 302 N TYR A 86 SHEET 4 AA2 7 GLN A 9 ARG A 18 1 N ILE A 15 O ILE A 303 SHEET 5 AA2 7 ALA A 335 VAL A 342 -1 O PHE A 338 N VAL A 14 SHEET 6 AA2 7 PRO A 348 TYR A 356 -1 O TYR A 349 N TRP A 341 SHEET 7 AA2 7 CYS A 393 PRO A 394 -1 O CYS A 393 N VAL A 350 SHEET 1 AA3 2 ARG A 198 ALA A 200 0 SHEET 2 AA3 2 ALA A 209 GLU A 211 -1 O ALA A 209 N ALA A 200 SSBOND 1 CYS A 79 CYS A 110 1555 1555 2.04 SSBOND 2 CYS A 135 CYS A 410 1555 1555 2.05 SSBOND 3 CYS A 180 CYS A 189 1555 1555 2.00 SSBOND 4 CYS A 384 CYS A 393 1555 1555 2.11 LINK O GLN A 230 K K A 504 1555 1555 2.76 LINK O GLY A 231 K K A 504 1555 1555 2.73 LINK O1 IHS A 502 K K A 504 1555 1555 2.86 LINK O4 IHS A 502 K K A 504 1555 1555 2.69 LINK O13 IHS A 502 K K A 504 1555 1555 2.89 LINK O15 IHS A 502 K K A 504 1555 1555 3.03 LINK O35 IHS A 502 K K A 504 1555 1555 2.87 LINK O43 IHS A 502 K K A 504 1555 1555 2.74 SITE 1 AC1 21 ARG A 18 HIS A 19 ARG A 22 THR A 25 SITE 2 AC1 21 LYS A 26 ARG A 94 HIS A 128 THR A 219 SITE 3 AC1 21 GLU A 222 PHE A 257 HIS A 306 ASP A 307 SITE 4 AC1 21 HOH A 612 HOH A 613 HOH A 651 HOH A 675 SITE 5 AC1 21 HOH A 693 HOH A 773 HOH A 803 HOH A 832 SITE 6 AC1 21 HOH A 867 SITE 1 AC2 19 PRO A 43 LYS A 45 TYR A 48 THR A 50 SITE 2 AC2 19 PRO A 51 ARG A 52 GLN A 230 GLY A 231 SITE 3 AC2 19 MET A 232 LYS A 347 K A 504 HOH A 625 SITE 4 AC2 19 HOH A 635 HOH A 716 HOH A 732 HOH A 774 SITE 5 AC2 19 HOH A 789 HOH A 871 HOH A 872 SITE 1 AC3 9 PHE A 257 ARG A 262 SER A 314 THR A 320 SITE 2 AC3 9 TRP A 321 ASN A 329 THR A 330 HOH A 689 SITE 3 AC3 9 HOH A 752 SITE 1 AC4 3 GLN A 230 GLY A 231 IHS A 502 CRYST1 82.300 82.300 103.620 90.00 90.00 120.00 P 32 2 1 6 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 0.012151 0.007015 0.000000 0.00000 SCALE2 0.000000 0.014030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009651 0.00000