PDB Short entry for 1ZEF HEADER HYDROLASE 18-APR-05 1ZEF TITLE STRUCTURE OF ALKALINE PHOSPHATASE FROM HUMAN PLACENTA IN COMPLEX WITH TITLE 2 ITS UNCOMPETITIVE INHIBITOR L-PHE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKALINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PLAP-1, REGAN ISOZYME; COMPND 5 EC: 3.1.3.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: PLACENTA KEYWDS ALKALINE PHOSPHATASE, UNCOMPETITIVE INHIBITOR, INTERMEDIATE STATE, L- KEYWDS 2 PHE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.LLINAS,E.A.STURA,A.MENEZ,Z.KISS,T.STIGBRAND,J.L.MILLAN,M.H.LE DU REVDAT 4 29-JUL-20 1ZEF 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-JUL-11 1ZEF 1 VERSN REVDAT 2 24-FEB-09 1ZEF 1 VERSN REVDAT 1 28-JUN-05 1ZEF 0 JRNL AUTH P.LLINAS,E.A.STURA,A.MENEZ,Z.KISS,T.STIGBRAND,J.L.MILLAN, JRNL AUTH 2 M.H.LE DU JRNL TITL STRUCTURAL STUDIES OF HUMAN PLACENTAL ALKALINE PHOSPHATASE JRNL TITL 2 IN COMPLEX WITH FUNCTIONAL LIGANDS. JRNL REF J.MOL.BIOL. V. 350 441 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15946677 JRNL DOI 10.1016/J.JMB.2005.04.068 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39871 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2115 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2897 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1390 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.1950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3669 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 702 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : 0.83000 REMARK 3 B33 (A**2) : -0.53000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.181 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3806 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3391 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5161 ; 1.720 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7865 ; 1.075 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 6.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 564 ; 0.175 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4292 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 781 ; 0.024 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1052 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4719 ; 0.264 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2383 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 593 ; 0.209 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 9 ; 0.164 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 35 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 205 ; 0.310 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 79 ; 0.311 ; 0.200 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): 2397 ; 0.913 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3824 ; 1.679 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1409 ; 2.862 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1337 ; 4.626 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1ZEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43024 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: FFT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 53.17050 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 53.17050 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 43.89550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.47200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.89550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.47200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.17050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.89550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.47200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.17050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.89550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.47200 REMARK 290 SMTRY3 8 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 87.79100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.17050 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 THR A 482 REMARK 465 THR A 483 REMARK 465 ASP A 484 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 ILE A 1 CG1 CG2 CD1 REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLN A 30 CG CD OE1 NE2 REMARK 470 ASP A 61 CG OD1 OD2 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 GLU A 469 CG CD OE1 OE2 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 1137 O HOH A 1488 1.88 REMARK 500 NH2 ARG A 301 O HOH A 1592 1.91 REMARK 500 O HOH A 1064 O HOH A 1367 1.92 REMARK 500 O HOH A 1279 O HOH A 1591 1.94 REMARK 500 O HOH A 1341 O HOH A 1550 1.98 REMARK 500 O HOH A 1290 O HOH A 1443 2.01 REMARK 500 O HOH A 1318 O HOH A 1508 2.05 REMARK 500 O6 NAG A 801 O HOH A 1513 2.10 REMARK 500 O HOH A 1109 O HOH A 1504 2.12 REMARK 500 O HOH A 1246 O HOH A 1532 2.12 REMARK 500 O HOH A 1235 O HOH A 1593 2.15 REMARK 500 O HOH A 1104 O HOH A 1200 2.18 REMARK 500 O HOH A 1252 O HOH A 1332 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 1068 O HOH A 1068 3655 1.34 REMARK 500 O HOH A 1042 O HOH A 1570 3655 1.93 REMARK 500 O HOH A 1062 O HOH A 1062 3655 1.94 REMARK 500 O HOH A 1439 O HOH A 1548 3655 1.95 REMARK 500 O HOH A 1089 O HOH A 1429 3655 2.17 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 10 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 220 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 301 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 301 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 349 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 385 CG - CD - NE ANGL. DEV. = 13.0 DEGREES REMARK 500 ARG A 385 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 428 CB - CG - OD2 ANGL. DEV. = 5.6 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 LYS A 60 -154.08 -85.28 REMARK 500 PHE A 107 122.06 -34.76 REMARK 500 SER A 359 -163.30 -107.89 REMARK 500 VAL A 361 45.70 -83.44 REMARK 500 ALA A 473 40.72 -90.29 REMARK 500 ASP A 475 40.93 -100.31 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 ASP A 61 LYS A 62 -140.60 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 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 42 OD1 REMARK 620 2 SEP A 92 OG 122.3 REMARK 620 3 SEP A 92 O3P 96.4 68.3 REMARK 620 4 ASP A 357 OD2 99.0 85.5 153.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 42 OD2 REMARK 620 2 SER A 155 OG 87.6 REMARK 620 3 GLU A 311 OE2 97.9 86.8 REMARK 620 4 HOH A 907 O 88.6 174.2 98.1 REMARK 620 5 HOH A 938 O 175.8 90.4 85.7 93.0 REMARK 620 6 HOH A 957 O 98.1 85.8 162.0 90.4 78.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SEP A 92 O3P REMARK 620 2 ASP A 316 OD1 80.3 REMARK 620 3 ASP A 316 OD2 82.9 58.2 REMARK 620 4 HIS A 320 NE2 171.3 91.4 95.0 REMARK 620 5 HIS A 432 NE2 89.8 152.1 94.9 98.8 REMARK 620 6 PHE A 802 N 72.3 101.7 150.9 107.2 99.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 904 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 216 OE1 REMARK 620 2 GLU A 216 OE2 56.7 REMARK 620 3 PHE A 269 O 83.1 139.5 REMARK 620 4 GLU A 270 OE2 99.2 94.9 86.9 REMARK 620 5 ASP A 285 OD1 160.9 142.2 78.2 83.7 REMARK 620 6 ASP A 285 OD2 142.8 89.0 130.9 97.6 54.1 REMARK 620 7 HOH A1158 O 84.5 92.1 87.6 173.0 90.9 82.7 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EW2 RELATED DB: PDB REMARK 900 ALKALINE PHOSPHATASE FROM HUMAN PLACENTA : NATIVE REMARK 900 RELATED ID: 1ZEB RELATED DB: PDB REMARK 900 ALKALINE PHOSPHATASE FROM HUMAN PLACENTA IN COMPLEX WITH 5'-AMP REMARK 900 RELATED ID: 1ZED RELATED DB: PDB REMARK 900 ALKALINE PHOSPHATASE FROM HUMAN PLACENTA IN COMPLEX WITH P- REMARK 900 NITROPHENYL-PHOSPHONATE DBREF 1ZEF A 1 484 UNP P05187 PPB1_HUMAN 23 506 SEQRES 1 A 484 ILE ILE PRO VAL GLU GLU GLU ASN PRO ASP PHE TRP ASN SEQRES 2 A 484 ARG GLU ALA ALA GLU ALA LEU GLY ALA ALA LYS LYS LEU SEQRES 3 A 484 GLN PRO ALA GLN THR ALA ALA LYS ASN LEU ILE ILE PHE SEQRES 4 A 484 LEU GLY ASP GLY MET GLY VAL SER THR VAL THR ALA ALA SEQRES 5 A 484 ARG ILE LEU LYS GLY GLN LYS LYS ASP LYS LEU GLY PRO SEQRES 6 A 484 GLU ILE PRO LEU ALA MET ASP ARG PHE PRO TYR VAL ALA SEQRES 7 A 484 LEU SER LYS THR TYR ASN VAL ASP LYS HIS VAL PRO ASP SEQRES 8 A 484 SEP GLY ALA THR ALA THR ALA TYR LEU CYS GLY VAL LYS SEQRES 9 A 484 GLY ASN PHE GLN THR ILE GLY LEU SER ALA ALA ALA ARG SEQRES 10 A 484 PHE ASN GLN CYS ASN THR THR ARG GLY ASN GLU VAL ILE SEQRES 11 A 484 SER VAL MET ASN ARG ALA LYS LYS ALA GLY LYS SER VAL SEQRES 12 A 484 GLY VAL VAL THR THR THR ARG VAL GLN HIS ALA SER PRO SEQRES 13 A 484 ALA GLY THR TYR ALA HIS THR VAL ASN ARG ASN TRP TYR SEQRES 14 A 484 SER ASP ALA ASP VAL PRO ALA SER ALA ARG GLN GLU GLY SEQRES 15 A 484 CYS GLN ASP ILE ALA THR GLN LEU ILE SER ASN MET ASP SEQRES 16 A 484 ILE ASP VAL ILE LEU GLY GLY GLY ARG LYS TYR MET PHE SEQRES 17 A 484 ARG MET GLY THR PRO ASP PRO GLU TYR PRO ASP ASP TYR SEQRES 18 A 484 SER GLN GLY GLY THR ARG LEU ASP GLY LYS ASN LEU VAL SEQRES 19 A 484 GLN GLU TRP LEU ALA LYS ARG GLN GLY ALA ARG TYR VAL SEQRES 20 A 484 TRP ASN ARG THR GLU LEU MET GLN ALA SER LEU ASP PRO SEQRES 21 A 484 SER VAL THR HIS LEU MET GLY LEU PHE GLU PRO GLY ASP SEQRES 22 A 484 MET LYS TYR GLU ILE HIS ARG ASP SER THR LEU ASP PRO SEQRES 23 A 484 SER LEU MET GLU MET THR GLU ALA ALA LEU ARG LEU LEU SEQRES 24 A 484 SER ARG ASN PRO ARG GLY PHE PHE LEU PHE VAL GLU GLY SEQRES 25 A 484 GLY ARG ILE ASP HIS GLY HIS HIS GLU SER ARG ALA TYR SEQRES 26 A 484 ARG ALA LEU THR GLU THR ILE MET PHE ASP ASP ALA ILE SEQRES 27 A 484 GLU ARG ALA GLY GLN LEU THR SER GLU GLU ASP THR LEU SEQRES 28 A 484 SER LEU VAL THR ALA ASP HIS SER HIS VAL PHE SER PHE SEQRES 29 A 484 GLY GLY TYR PRO LEU ARG GLY SER SER ILE PHE GLY LEU SEQRES 30 A 484 ALA PRO GLY LYS ALA ARG ASP ARG LYS ALA TYR THR VAL SEQRES 31 A 484 LEU LEU TYR GLY ASN GLY PRO GLY TYR VAL LEU LYS ASP SEQRES 32 A 484 GLY ALA ARG PRO ASP VAL THR GLU SER GLU SER GLY SER SEQRES 33 A 484 PRO GLU TYR ARG GLN GLN SER ALA VAL PRO LEU ASP GLU SEQRES 34 A 484 GLU THR HIS ALA GLY GLU ASP VAL ALA VAL PHE ALA ARG SEQRES 35 A 484 GLY PRO GLN ALA HIS LEU VAL HIS GLY VAL GLN GLU GLN SEQRES 36 A 484 THR PHE ILE ALA HIS VAL MET ALA PHE ALA ALA CYS LEU SEQRES 37 A 484 GLU PRO TYR THR ALA CYS ASP LEU ALA PRO PRO ALA GLY SEQRES 38 A 484 THR THR ASP MODRES 1ZEF ASN A 122 ASN GLYCOSYLATION SITE MODRES 1ZEF ASN A 249 ASN GLYCOSYLATION SITE MODRES 1ZEF SEP A 92 SER PHOSPHOSERINE HET SEP A 92 10 HET NAG A 801 14 HET PHE A 802 12 HET NAG A 803 14 HET PHE A 804 12 HET ZN A 901 1 HET ZN A 902 1 HET MG A 903 1 HET CA A 904 1 HETNAM SEP PHOSPHOSERINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM PHE PHENYLALANINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 PHE 2(C9 H11 N O2) FORMUL 6 ZN 2(ZN 2+) FORMUL 8 MG MG 2+ FORMUL 9 CA CA 2+ FORMUL 10 HOH *702(H2 O) HELIX 1 1 PRO A 3 GLU A 7 5 5 HELIX 2 2 ASN A 8 LEU A 26 1 19 HELIX 3 3 GLY A 45 LYS A 60 1 16 HELIX 4 4 ALA A 70 PHE A 74 5 5 HELIX 5 5 ASP A 91 GLY A 102 1 12 HELIX 6 6 GLN A 120 THR A 124 5 5 HELIX 7 7 SER A 131 ALA A 139 1 9 HELIX 8 8 HIS A 153 GLY A 158 1 6 HELIX 9 9 SER A 170 VAL A 174 5 5 HELIX 10 10 PRO A 175 GLU A 181 1 7 HELIX 11 11 ASP A 185 ASN A 193 1 9 HELIX 12 12 ARG A 204 PHE A 208 5 5 HELIX 13 13 ASP A 220 GLY A 224 5 5 HELIX 14 14 ASN A 232 LYS A 240 1 9 HELIX 15 15 ASN A 249 LEU A 258 1 10 HELIX 16 16 TYR A 276 ARG A 280 5 5 HELIX 17 17 SER A 287 SER A 300 1 14 HELIX 18 18 ARG A 314 GLU A 321 1 8 HELIX 19 19 ARG A 323 THR A 345 1 23 HELIX 20 20 THR A 410 GLY A 415 1 6 HELIX 21 21 GLN A 445 VAL A 449 5 5 HELIX 22 22 THR A 456 ALA A 466 1 11 SHEET 1 A10 ALA A 244 VAL A 247 0 SHEET 2 A10 HIS A 264 LEU A 268 1 O MET A 266 N ARG A 245 SHEET 3 A10 VAL A 198 GLY A 202 1 N ILE A 199 O GLY A 267 SHEET 4 A10 SER A 142 ARG A 150 1 N THR A 149 O GLY A 202 SHEET 5 A10 PHE A 306 GLY A 312 1 O PHE A 309 N GLY A 144 SHEET 6 A10 ASN A 35 GLY A 41 1 N LEU A 40 O VAL A 310 SHEET 7 A10 THR A 350 ALA A 356 1 O LEU A 353 N PHE A 39 SHEET 8 A10 VAL A 437 ARG A 442 -1 O ARG A 442 N SER A 352 SHEET 9 A10 TYR A 76 LYS A 81 -1 N TYR A 76 O ALA A 441 SHEET 10 A10 VAL A 452 GLU A 454 1 O GLN A 453 N LEU A 79 SHEET 1 B 2 SER A 359 HIS A 360 0 SHEET 2 B 2 HIS A 432 ALA A 433 -1 O ALA A 433 N SER A 359 SHEET 1 C 3 PHE A 362 PHE A 364 0 SHEET 2 C 3 LEU A 391 ASN A 395 -1 O LEU A 392 N SER A 363 SHEET 3 C 3 SER A 423 VAL A 425 1 O ALA A 424 N GLY A 394 SSBOND 1 CYS A 121 CYS A 183 1555 1555 2.06 SSBOND 2 CYS A 467 CYS A 474 1555 1555 2.06 LINK C ASP A 91 N SEP A 92 1555 1555 1.32 LINK C SEP A 92 N GLY A 93 1555 1555 1.32 LINK ND2 ASN A 122 C1 NAG A 801 1555 1555 1.43 LINK ND2 ASN A 249 C1 NAG A 803 1555 1555 1.47 LINK OD1 ASP A 42 ZN ZN A 902 1555 1555 1.89 LINK OD2 ASP A 42 MG MG A 903 1555 1555 2.01 LINK O3P SEP A 92 ZN ZN A 901 1555 1555 2.16 LINK OG SEP A 92 ZN ZN A 902 1555 1555 2.10 LINK O3P SEP A 92 ZN ZN A 902 1555 1555 2.17 LINK OG SER A 155 MG MG A 903 1555 1555 2.17 LINK OE1 GLU A 216 CA CA A 904 1555 1555 2.21 LINK OE2 GLU A 216 CA CA A 904 1555 1555 2.40 LINK O PHE A 269 CA CA A 904 1555 1555 2.22 LINK OE2 GLU A 270 CA CA A 904 1555 1555 2.14 LINK OD1 ASP A 285 CA CA A 904 1555 1555 2.51 LINK OD2 ASP A 285 CA CA A 904 1555 1555 2.22 LINK OE2 GLU A 311 MG MG A 903 1555 1555 1.96 LINK OD1 ASP A 316 ZN ZN A 901 1555 1555 2.02 LINK OD2 ASP A 316 ZN ZN A 901 1555 1555 2.37 LINK NE2 HIS A 320 ZN ZN A 901 1555 1555 2.12 LINK OD2 ASP A 357 ZN ZN A 902 1555 1555 2.07 LINK NE2 HIS A 432 ZN ZN A 901 1555 1555 2.00 LINK N PHE A 802 ZN ZN A 901 1555 1555 2.20 LINK MG MG A 903 O HOH A 907 1555 1555 2.12 LINK MG MG A 903 O HOH A 938 1555 1555 2.07 LINK MG MG A 903 O HOH A 957 1555 1555 2.06 LINK CA CA A 904 O HOH A1158 1555 1555 2.27 CISPEP 1 GLU A 469 PRO A 470 0 1.23 CRYST1 87.791 114.944 106.341 90.00 90.00 90.00 C 2 2 21 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 0.011391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009404 0.00000